As the Red Skull revealed the Soul Stone can only be retrieved by someone sacrificing something they love and contrary to Gamoras belief Thanos truly did love her albeit in a twisted way.
Why did thanos cry when he killed gamora. But in the movies its established that Thanos himself is the one who killed the Zehoberei giving their relationship an intense and complex twist with an icky undercurrent of emotional abuse. The dynamic between Thanos Josh Brolin and Gamora Zoe Saldana was one of the main story arcs of Avengers. My guess as to the cause of his favoritism of her would be that she was both the first one he adopted and because of how fearless and strong she seemed as a child.
Gamora placed the Power Stone in the hilt of her sword and used it to kill Thanos and has now come to gather the other Infinity Stones to retrieve the piece of her soul that is still trapped inside of the Soul Stone. In the movie Avengers. While everyone is still reeling from the revelation Gamora stabs Star-Lord in the chest seemingly killing him too.
In his mind it probably reminded him of himself and it gave him hope that someone might be able to truly understand his reasons for what he does and that. In order to get Gamora to divulge the location of the Soul Stone he tortures Nebula right in front of Gamora. Viewed 6k times.
Infinity War there is a scene on Knowhere where Gamora tries and manages to kill Thanos and before he asks Why did you do this my child. In the MCUs Guardians of the Galaxy it first became clear that while Thanos had adopted both Nebula and Gamora as daughters he had a clear favorite - and the reason lay more in himself than in them. On a dead world.
While Gamora keeps crying. And whats more he was visibly crying when he had to kill her in Infinity War. Though she attempts suicide before he can make the necessary sacrifice Thanos is.
Thanos tells Peter to kill Gamora but when Peter decides to pull the trigger a flurry of bubbles leaves his gun in lieu of a energy blast. Thanos mourns Gamora s death Tearfully Thanos apologized to Gamora for what he was about to do before grabbing her arm and dragging her screaming towards the edge of the cliff. Despite his reluctance and her frantic screams Thanos threw Gamora off the cliff to her death.