The invention discloses a hybrid energy storage optimal power allocation method with state-of-charge deviation being taken into consideration. The method comprises the following steps: calculating leveling offset amount: carrying out multi-scale decomposition through an a'trous algorithm based on wavelet transform to obtain separated offset amount time sequence, and independently bearing high-frequency and low-frequency components of the leveling offset amount through power-type and energy-type energy storage mediums; serving a lithium battery LiB and a super-capacitor Uc as hybrid energy storage forming mediums, and with state-of-charge SOC leading factors influencing HESS operation being taken into consideration, building an optimal model for an objective function with the state-of-charge SOC offset variance being the minimum as the target; establishing a charge/discharge power distribution mode of the hybrid energy storage medium with charge/discharge power and capacity limit constraints being taken into consideration; and carrying out example analysis according to actual wind power station data. The calculation result shows that method can effectively realize efficient control of a hybrid energy storage system, and has a certain practical application value.