Provided are a card payment method and system through application linkage. More particularly, provided are a card payment method and system through application linkage, wherein applications are installed on a payment terminal and a user terminal, a payment card is linked to the application on the user terminal, an application server manages the linkage, and in the case of a payment transaction, the application server performs a relay between the payment terminal and the user terminal so that transaction information input to the payment terminal is checked with the user terminal, and the payment terminal completes the transaction with a signature and tip setting input to the user terminal.