He can't bring himself to do it. Jedi can't have children, and Anakin was the closest thing Obi-Wan had to a son. Despite the shitty prequels glossing over the relationship, he raised Anakin like a son, and watched him grow from a little boy into a man before the Dark Side stole him away. No matter how evil he became, and no matter what he did, in his heart, Anakin was still that little boy that he believed, likely correctly, that he failed.
In the battle, notice that he does seem prepared to kill Darth Vader, and it isn't until his mask is cut open and he sees and hears Anakin that the doubt creeps in and ultimately wins. Suddenly he wasn't fighting a robot monster, but he was about to murder someone he raised like a son.
Love is the most powerful force there is, both in the real world and the world of Star Wars. Consider the finale to the original trilogy. Anakin, who has been pure evil since he was a teen-- he murdered children, destroyed the Jedi Order, and ruled the galaxy as head of an evil empire-- sees his son, a son he only recently learned he had, and one he'd never laid eyes on for the first 18 years of his life, about to die, and has a complete change of heart. His love for his son is strong enough to eradicate the Dark Force from his soul, and he redeems himself before he dies.
Obi-Wan felt a similar love, and could not strike the final blow to kill Anakin.
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