Developing van der Waals (vdW) heterostructures is an excellent approach for optimizing exceptional optoelectronic and photocatalytic properties of materials; therefore, researching the interface dynamics of charge carriers at the two-dimensional vdW heterojunction is of great significance. In this work, we perform time-dependent ab initio non-adiabatic molecular dynamics simulations to study the dynamics of charge transfer at the B4C3/g-C3N4 heterostructure. The simulations show that the charge transfer between B4C3/g-C3N4 layers is mainly caused by the non-adiabatic mechanism. The non-adiabatic mechanism leads to a higher charge-transfer efficiency and slows down the process of interlayer electron-hole recombination, thereby promoting the separation of photogenerated electron-hole pairs. Our investigation provides essential insights into understanding the dynamics of charge transfer for the B4C3/g-C3N4 heterostructure, which provides guidance for photocatalytic water splitting and optoelectrical applications.