This paper analyzes information security in the E-commerce based on game theory, and this game analysis method is applied to information security for the first time. We set up the information security game model of the defender and the attacker, make the equilibrium analysis of this game model, and get the ideal strategy combination. Then we introduce the penalty parameter of the defender and the penalty parameter of the attacker to solve the problem that the restriction condition is not satisfied. The introduction of the penalty parameter of the defender promotes the defender to invest in information security, and the introduction of the penalty parameter of the attacker promotes the attacker to take no attack strategy. This paper provides good reference for information security in the E-commerce.