A large-scale three-dimensional physical model test system for a deep cavern group comprises a base, an anti-deformation prestressed loading frame assembly, a load applying assembly, a model sample preparation and transportation assembly and a multifunctional hydraulic loading system assembly. The anti-deformation prestressed loading frame assembly and the model sample preparation and transportation assembly are both arranged on the base. The load applying assembly is arranged on the anti-deformation prestressed loading frame assembly, and the load applying assembly is connected with the multifunctional hydraulic loading system assembly. A model sample is subjected to long-time load holding, dynamic disturbance and displacement control overload under multi-surface multi-point cooperative control through cooperation between the load applying assembly and the multifunctional hydraulic loading system assembly.