Bill Nye the Science Guy is having a bad reaction to his old TV partners at Disney, which is why he's suing them for $9 million!

Bill filed docs Thursday in L.A., saying Disney -- which marketed and distributed his show -- cut him a check in 2008 for back-end profits. The check was for $585k, but a couple months later he says Disney drastically changed it's story ... and claimed he needed to return $496,000!

According to the docs, Disney told Bill it made an accounting error, and informed him he wouldn't get any future checks until it recouped the $496k. 

All of this made Bill suspicious, and he called for an audit of Disney's book in 2016. In the docs, Bill says the auditor found he'd been shorted by $9.3 mil since signing his deal in 1993.

Bill's now retained attorneys at Hamrick & Evans to get his dough. We reached out to Disney, but no word back.

Side note: Science, apparently, pays like a mutha! Who knew Bill was such a baller??