The variational theory is an inextricable part of both continuum mechanics and physics, and plays an important role in mathematics and nonlinear science, however it is difficult to find a variational formulation for a nonlinear system, and it is more difficult for a fractional differential system. This paper is to search for a variational formulation for the Schrödinger-KDV system with M-fractional derivatives. The fractional complex transformation is used to convert the system into a traditional differential system, and the semi-inverse method is further applied to establish a needed variational principle.