The invention discloses an energy control method for an independent photovoltaic hybrid energy storage system. The hybrid energy storage system comprises a storage battery, a super capacitor, a photovoltaic power generation unit, a DC bus and a DC load. The storage battery and the super capacitor are connected in parallel with the DC bus through respective bidirectional DC/DC converters. The photovoltaic power generation unit is connected to the DC bus through a BOOST converter. After data acquisition, an energy control processor calculates the power that should be borne by the hybrid energy storage system, and then the power passes through a first-order low-pass filter. According to limit control methods of different sections, the hybrid energy storage system, under different control conditions, achieves power distribution to the storage battery and the super capacitor, maintains the stability of the DC bus, stabilizes photovoltaic output power fluctuation, maintains in-system power balance, optimizes the work of energy storage equipment to a certain extent, and prolongs the service life of the energy storage equipment.