The invention discloses a method and a system of safety protection of a Web application. According to the method and the system, the method comprises the following steps that: an administrator configures a protection rule on a Web client according to the need, so that a protection rule file is formed, the protection rule file is arranged in a safety protection module of a server, and a global filter is provided; when a Web application server receives a Web application access request of a user, the safety protection module compares request data of the Web application access request and the configured protection rule file and checks whether the request data is matched with the protection rule file, if so, the Web application access is intercepted; and otherwise, the Web application access is allowed. According to the method and the system, which are disclosed by the invention, all Web applications can be protected according to the need, so that safety of the Web access is improved. The intercept action of the Web application access is transferred into a proxy service server from an application program, so that repeated development or missing intercept of the application program is avoided, and the cost is reduced.