I watched House MD series complete, but couldn't figure out why did Stacy left House after the operation.
I don't believe we see much more of House and Stacy's relationship after the operation, but what we see in "Three Stories" very strongly implies that Stacy didn't leave House -- House left her. Remember, she knew he wanted the riskier, more painful surgery that would have left him with full use of his leg. Her choice to change the surgery, after he was unconscious, was a betrayal of his trust.
It's also likely that his newly-acquired painkiller addiction played a part; at the very least, it would have caused problems during any possible attempts at reconciliation. We don't know if, or how hard, Stacy tried to reconcile with House, but his emotional and mental state would have been affected by the drugs, making everything more difficult.
(Whatever details there are behind their break-up, they couldn't have been too bad. At first she's reluctant to ask for his help, and he's reluctant to give it, but she does, and he does. I assume this means they parted on terms that were at least politely cordial.)