For the three-port DC/DC converter in the microgrid energy storage system, the predictive current phase shift control based on half switching cycle sampling and full switching cycle sampling is studied. The working state and switching mode of the converter are analyzed. The slope of the inductor current is obtained by Y-D equivalent transformation. The inductor current is sampled at the midpoint of the driving signal of each switching cycle, and the inductor current increment of the converter at different stages is calculated. Based on the current sampling value and the current reference value, the phase shift ratios of rising edge and falling edge for the next switching cycle of the converter are predicted. By updating the phase shift ratios, the inductor current can reach the reference value. Then the elimination mechanism of DC component in the inductor current in two sampling modes is analyzed, and the closed-loop control strategy of three-port DC/DC converter is given. The simulation results verify the effectiveness of the proposed control method and solve the DC bias problem of the three-port DC/DC converter, which improves the dynamic response and robust performance of the system. This work is supported by National Key Research and Development Program of China (No. 2017YFB0903100) Science and Technology Project of State Grid Corporation of China (No. 521104170043).