Standalone microgrid is an effective way to solve the problem of power supply in remote areas. However, standalone microgrid is lack of the support of large power grid and its frequency modulation capability and frequency stability are relatively weak. It is necessary to consider the frequency modulation in microgrid planning. Under the background, in view of the dual needs of peak modulation and frequency modulation, this paper proposes an investment optimization method of standalone microgrid that takes into account frequency modulation with hybrid energy storage. Firstly, the correlative mechanism and logical relationship of source and storage configuration parameters satisfying the requirements of frequency and peak regulation are studied. Then, an optimal allocation investment model of standalone microgrid is established with the objective of minimizing the total cost of system investment under the main constraints of wind abandonment rate and load power shortage rate. The model is solved by genetic algorithm. Lastly, an island microgrid is taken as the background for example analysis. The results show that the proposed method effectively considers demand of frequency modulation and peak modulation, and realize the integrated optimal allocation of source and storage.