Why Daenerys Killed Varys?

Varys, of course, was executed shortly after that for committing treason against Daenerys by supporting Jon's claim to the Iron Throne and trying to poison her.

Why did Daenerys kill Lord Varys?

Daenerys literally warned him she'd kill him if he did this. Sure, he warned her as he vowed to, but part of that promise was also not to conspire behind her back. Varys said he was always a servant to the people, not rulers.

Why did Varys betray Daenerys?

He's been watching his queen carefully for quite some time now, and before his death, he's certain that she's not fit to rule the Seven Kingdoms. Varys betrays Daenerys because he's only ever had one motivation: to protect the realm. Varys himself says he's served more rulers than anyone else in the Seven Kingdoms.