Schema theorem is the theoretical foundation of the evolutionary algorithm. This paper focuses on a new, and general schema theory for multigenic chromosomes gene expression programming. The theory is applicable to every operator in GEP via the method of probability. Not only the destruction but also the creation probability of the schema is considered in the evolutionary process. An equivalent form of general schema theory of GEP was deduced. The result shows that the individuals with high fitness values, shorter schema order, more function nodes, and the shorter the insertion sequence have the greater transmission probability than the average ones.