The present disclosure is related to a power module power structure and an assembling method thereof. The power module structure includes a first printed-circuit-board (PCB) assembly, a second PCB assembly, and a conductive connection component. The first PCB assembly includes a first circuit board, a power switch and a magnetic component. The first circuit board includes a first side, a second side and a through hole. The power switch is disposed on the first circuit board. The magnetic component includes a first magnetic core and a second magnetic core fastened on the first circuit board through the through hole. The second PCB assembly includes a second circuit board having a third side, a fourth side and a hollow slot passing therethrough. The second magnetic core is exposed through the hollow slot. The conductive connection component is disposed and electrically connected between the first PCB assembly and the second PCB assembly.