The invention discloses a tax withholding and paying system for confirming payment according to secondary identity identification of a tax payment identification code. The system comprises a third-party payment platform, a bank account, user main bodies registered by using the tax payment identification code, a government tax institution account and a government pension medical insurance account.Secondary identification confirmation charging refers to high-speed charging, bus and subway charging, parking lot charging and the like which need to judge the amount and confirm the identity according to the distance or duration. The identity confirmation needs to bind a license plate according to the tax payment identification code, or a fingerprint or a face of a user, identity recognition hardware is scanned twice through an initial terminal and an end terminal to confirm that payment should be carried out, and the third-party payment platform withdraws tax fee for payment according to the tax recognition code and transfers the tax fee to a related charging company account, a government tax institution account and a government pension medical insurance fund account.