To address the problem of high battery usage throughout the year, an empirical modal decomposition-based optimal allocation method for PV microgrid energy storage capacity is designed. This paper describes the basic structure of the photovoltaic equivalent circuit to obtain the output power of the photovoltaic microgrid panel. We use the energy storage battery as a secondary power source to smooth the photovoltaic power output and calculate the wasted power. In this paper, an energy management model based on empirical mode decomposition is constructed, and the photovoltaic power generation unit and energy storage unit are regarded as optimally configured whole. Based on the above conditions, an optimal allocation method of energy storage capacity is designed. Experimental results: the mean value of annual battery usage for the PV microgrid capacity optimization allocation method in the paper is: 53.74%, indicating that the designed PV microgrid capacity optimization allocation method is more feasible after combining the empirical modal decomposition algorithm.