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You didn't say which time you're talking about—how did she recognize Auton Rory in "The Pandorica Opens", how did she remember real Rory back into existence in "The Big Bang", how did she recognize Captain Williams in "The Wedding of River Song"…

But ultimately, it's probably the same in every case. First, there's the fact that Amy is a time traveler, and therefore can remember across the timelines (as explained in "Flesh and Stone"). Then there's the fact that Amy grew up with a time crack leaking into her head, giving her unique abilities (as explained in "The Big Bang"). And finally, there's the power of love.