The invention discloses a hybrid power system with vehicle-mounted fuel cells and lithium cells in direct parallel connection. An output end of a fuel cell generation device is connected with an input end of a motor controller through a first switch conductive device; an output end of a lithium cell pack is connected with the input end of the motor controller through a second switch conductive device; an output end of the motor controller is connected with a motor; and a system energy management controller is respectively connected with a fuel cell controller, a lithium cell management system, the motor controller, a control end of the first switch conductive device and a control end of the second switch conductive device and used for controlling the ON and OFF of the first switch conductive device and controlling the forward ON or the backward ON or OFF of the second switch conductive device according to information obtained by the fuel cell controller and the lithium cell managementsystem. In the system, the traditional power supply mode requiring DC/DC (Direct Current/Direct Current) voltage stabilization is abandoned, the power supply efficiency is improved, the voltage fluctuation of the fuel cell generation device is shared by the lithium cell pack and the fuel cells protected.