The invention provides a multi-layered aquifer underground flow system-based underground water pollution simulator, which comprises a simulation groove, a pressure measurement device, water head adjustment devices and a rainfall device, wherein the simulation groove comprises a seepage groove, an upstream water tank and a downstream water tank which are positioned on two sides of the seepage groove; front and back sides of the seepage groove are respectively provided with uniformly distributed sampling holes and pressure measurement holes, and the pressure measurement holes are connected with the pressure measurement device; two water head adjustment devices correspond to the upstream water tank and the downstream water tank respectively, and each water head adjustment device comprises a bracket, an overflow box, a water pipe and a lift rod; the rainfall device is positioned above the seepage groove, rainfall holes are uniformly distributed on a pipeline of the rainfall device; and one end of the pipeline is sealed, and the other end of the pipeline is connected with a water source. The multi-layered aquifer underground flow system-based underground water pollution simulator can simulate an underground waterflow system of a plurality of aquifers and aquitards, is convenient in measurement, and has small error.