A method and system for program protection based on a .NET card. The method includes compiling, by a first device, first source code into a first assembly, and storing the first assembly to a .NET card. Information of a remotely invoked class in the first source code is extracted to form a new class. A remote invocation instruction is written in the new class to generate second source code. The second source code is compiled into a second assembly, and the .NET card and the second assembly are provided to a second device. The second device executes the second assembly, remotely invoking the class in the first source code, executing the class at the .NET card via an interface of the .NET card, and receiving an execution result returned by the .NET card. The system includes a .NET card, a first device and a second device.