The invention discloses a testing method of a fluid-structure interaction analog simulation testing device. The testing method includes steps of firstly, filling a simulated stratum material in a simulated box body according to the lamellar distribution; filling water by a water filling device and simulating the water-containing layer; then horizontally pressurizing both sides of the simulation box body by a horizontal hydraulic loading system so as to simulate the confining pressure; at last, performing vertical pressure loading on the simulated box body by a vertical directional hydraulic loading system so as to simulate loads with different depths. The testing method of the fluid-structure interaction analog simulation testing device can be adapted to different experimental demands. The testing method can realize accurate pressure adjusting, simulate loads with different depths of the stratum, an apply uneven pressure.