The invention discloses an onboard high heating flux surface cooling system. A circulation system is formed by sequentially connecting an intermittent heat load surface, a second liquid storage device, a second pump, at least one phase-change heat storage device, a first liquid storage device, a filter, a first pump, an atomizing nozzle and the intermittent heat load surface through a pipeline. A refrigerant is arranged in the pipeline. The phase-change heat storage device is further provided with a cold source inlet and a cold source outlet. The onboard high heating flux surface cooling system has the beneficial effects that the size is small, the weight is small, the heat exchange effect is good, energy is saved, and pollution is avoided; meanwhile the structure is compact, and the manufacturing technology is simple; and the onboard high heating flux surface cooling system is suitable for cooling of high heating flux intermittent heat loads. The invention further discloses a working method of the onboard high heating flux surface cooling system.