I've been working on my current story for almost a year. It's a great story but at times it seems really complicated. How complicated is too complicated in a story?
Different readers like different things. What feels too complicated for one reader is intriguing for another. To evaluate your own book, there's two things you can do:
Be aware of what you write (your "genre", if you want). Now go and look in other books in your niche. How complicated are they and how does your book compare?
You may need to let your book rest for a while (i.e. not work on it) to gain the necessary distance to assess it objectively. That's why many professional writers work on the next book before they revise the previous one.
Find beta readers that are fans of your genre. Get feedback from (several of) them.
You can work on your next book, while your present project is with your beta readers.
Short answer: It depends.
Long answer: Complexity can be tied in to several factors in a story. Word count is one I like to use. Most books fall within a certain range of word count. The average novel is 75,000 words in length. Most publishers won't accept manuscripts that are over 100,000 words from new authors. Of course, this varies depending on what genre your story falls into, but as a rule of thumb, aim for 100,000 words. If your story is significantly longer, it may either be too complex or drag on too much.
Another method is to count the minimum number of 'important' characters in your story. Think of it like this: if you were summarizing the plot to someone who's never read your story, how many characters would you bring up, and how many could you leave out without drastically changing the plot? Having never done this method myself, I'm not sure how many 'main characters' would be too many-use common sense, though. Five or six integral people makes sense, but fifty-seven...see what I mean? After a certain point, too many important characters make your story overly-complex.
When writing a story, I like to count the number of 'strands.' I define strands as "the number of character perspectives that could easily be written as independent stories that are just as interesting/important as the protagonist." If every single character in your story, even if they're not too important, has deep/interesting perspectives, this might draw attention away from the plot/protagonist, making the story too complex.
As Ben has already stated, you should ask someone else to give feedback on your story. Getting a second perspective can be helpful, because if your readers think it's too complex, then it's probably too complex.
Complexity is not a bad thing--in fact, I enjoy reading complex stories with intricate plots. Don't worry about simplifying your story until you're done with the first draft and have already given it to someone to read. If you want to simplify it, start with scenes and characters that, while interesting, don't contribute too much to the plot.
Good luck with your writing!
Unfortunately there is no measure of complexity, so there isn't really anyway anyone can answer your literal question.
But I found that many of my stories were too complex. I realized this when I couldn't describe a story to anyone and have it make sense. Part of that was because I related any story I came up with at a very high resolution -- read as lots of details. I'd always miss something and have to go back and explain.
I solved that by imagining my stories at lower and lower resolutions until I could describe the crux of the story in one or two sentences.
For me, I discovered that when I conceptualized my stories as a series of events -- and then this happens, then this happens -- my narratives often lacked a conceptual internal structure. It was like was making up things to happen that I thought would advance the story, but ended up making everything too complicated. I could hardly keep track of things myself, let alone relate them to someone else. Those stories are my most boring pieces. They never held anyone's attention. Not even my own.
So, your story might be too complicated if it doesn't hold together. For instance, if you read your pages, and you lose interest. It might be too complicated. But that might also mean that the writing isn't as effective as it needs to be. That the sentences are meh. Or dialogue and setting is blah.
Another assessment is to explain the story to a friend or just yourself, out loud, without handwaving your way through any important part. If you can do that and its feels rationale then probably your story isn't too complex. If you find it difficult to relate the gist of your story or why events in the story are connected then it might be too complex.