A three-dimensional packaging structure and a packaging method of power devices. The packaging structure includes power devices, direct copper bonded substrates (i.e., DBC substrates), flexible printed circuit boards (i.e., FPC boards), bonding wires, heat dissipation substrates, decoupling capacitors, a heatsink with integrating the fan, shells, and forms a half-bridge circuit structure composed by the power devices. The power circuit structure is optimized, parasitic inductance in the commutation loop is reduced by mutual inductance cancellation, thus overvoltage and oscillation during the power device switching process can be reduced. Additionally, by using the flexible characteristic of the flexible PCB, a three-dimensional packaging structure is formed and power density is improved.