Development of the active metal species with high utilization and accessibility of oil macromoleculars is one of the critical factors affecting heterogeneous metal-based catalysts for production of biodiesel. Here, we synthesized two-dimensional graphitic carbon nitride supported molybdenum (xMo/g-C3N4) catalysts for the facile transesterification of waste cooking soybean oil. Various characterization results of these catalysts show the crystal structure of g-C3N4 is not destroyed, however, Mo oxides phase, containing Mo6+ and Mo5+ state, is detected on the surface of the Mo/g-C3N4 with much Mo-loading, and the ratio of Mo6+/Mo5+ increases significantly with the increasing Mo loading. As expected, compared with the neat g-C3N4 catalyst, the g-C3N4 supported Mo catalyst exhibits a better catalytic performance; especially the 10%Mo/g-C3N4 catalyst has the optimal waste cooking soybean oil conversion of 71.1% and biodiesel selectivity of 99.5%. Furthermore, the experimental parameters and catalytic reusability for the transesterification reaction over 10%Mo/g-C3N4 catalyst are investigated. Moreover, the possible deactivation mechanism and regeneration method of asprepared catalyst are also proposed. This work provides a valuable tactics for the production of clean and low-cost biodiesel from waste cooking soybean oil in the presence of efficient solid catalyst.