The joining of dissimilar materials, especially metals and glass, is widespread in various industrial products. Ultrafast laser welding of heterogeneous materials is a fast, clean, and non-contact technique that has been extensively studied in recent years. In this study, molecular dynamics methods are used for simulating the femtosecond laser action at the interface between aluminum and quartz glass. The simulation constructed a Lennard-Jones (LJ) interaction potential for quartz glass according to its melting point and elastic constants. The construction of the LJ interaction potential between aluminum and quartz glass is based on the adhesion work between the two materials, thus simplifying and accelerating the simulation process while maintaining the macroscopic properties. A small-scale molecular dynamics simulation of the femtosecond laser action at the aluminum and quartz glass interface is performed using the two-temperature model coupled to molecular dynamics method. After femtosecond laser irradiation, the local transient temperature in the welding zone and stress are as high as 10000 K and 20 GPa, respectively, and diffusive movement of aluminum atoms to the quartz glass side occurs. The continuous collision of high-temperature particles causes the mixing zone of aluminum and quartz glass to expand, and the center of the mixing zone of the two materials moves toward the quartz glass side. The simulation reveals the molecular dynamics evolution of the femtosecond laser-action aluminum-quartz glass interface on the picosecond time scale at the microscopic level, providing a theoretical basis for femtosecond laser welding of dissimilar materials.