The invention provides a fuzzy empirical mode decomposition based power generation control method with effects of storing energy and smoothening new energy. The method comprises the following steps of reading related operating data of new energy and energy storage batteries; based on the empirical mode decomposition, dividing a power signal into a plurality of intrinsic mode functions and a margin; calculating a smoothing order reference value obtained by a standardized modulus accumulative mean value under different intrinsic mode functions; smoothing the new energy output based on the smoothing order reference value to obtain a smoothing value of the new energy output; determining a power command value of an energy storage system, and performing power limitation on the power command value of the energy storage system; and regulating the smoothing order k according to the load state and the smooth output fluctuation ratio of the energy storage batteries. The fuzzy empirical mode decomposition based power generation control method, through the self-adaptive and real-time regulation on the smoothing order, can reach the effects of preventing the phenomena of overcharge and overdischarge of the energy storage system, keeping good performance of the energy storage system, as well as maintaining better effect in smoothening the new energy output.