Why did God punish the Canaanites through the conquest of the land?

If you're referring to the ban (החרם תרימם) in the Torah (Deuteronomy 7:2), the Torah itself gives the reason (Leviticus ch.18, and Deuteronomy ch.9 and 18). It was because of the wickedness of the Canaanites, who engaged in human sacrifice, sorcery, and every form of lewdness including bestiality.