The clubs have agreed eight permanent or loan deals over the past four years, more than any other two Premier League teams.
"Good relations? They want to kill us and we want to kill them," Emery told reporters on Sunday.
"It's not a good relationship, it's a deal for money and a deal for players. I am happy for Emiliano Martinez and Morgan Rogers and I know I am not happy for Chelsea."
The flow of transfers began after the consortium BlueCo took control of Chelsea in 2022.
England midfielder Rogers joined Chelsea in a reported £117 million ($158 million) move, and Alejandro Garnacho was loaned to Villa with a conditional obligation for the transfer to become permanent next year.
Striker Nicolas Jackson then joined Villa and goalkeeper Emiliano Martinez completed his switch to Stamford Bridge.
British media reported that Chelsea have spent more than £160 million on Villa players since 2022, while Villa have paid around £102 million for players moving in the other direction.
Villa host champions Arsenal in the Premier League on Monday.