The present invention discloses a method and apparatus for protecting .net programs, relating to software protection. The method mainly includes: selecting a binary code segment from a .net program; transforming the binary code segment, and removing it from the .net program; writing the binary code segment to a shell of the .net program, and writing a shell calling instruction to the .net program; and executing the .net program, and calling a .net virtual machine to execute the binary code segment. The apparatus includes a selecting module, a transforming and removing module, a writing module, and an executing module. The programs running on the .net platform can be protected simply by being transformed.