A novel amplitude-domain pulse-width modulation (AD-PWM) technique for three-phase energy stored quasi-Z-source (ES-qZSI) photovoltaic (PV) power system is proposed in this paper. The proposed modulation technique performs switching states and shoot-through behavior based on the relationship of size among three-phase voltages, showing the attractiveness of extreme simplicity and low computation. This paper further investigates the AD-PWM based three-phase PV power system. An active power control method integrated with reactive power compensation for the system in natural coordinate to avoid complicated calculation of trigonometric function. As a result, active power regulation integrated with reactive power compensation is fast and reliable. Compare with the state-of-arts of control schemes for ES-qZSI system utilizing techniques, the proposed control strategy has advantages: 1) The computation is low because there is no shoot-through reference and avoiding complexity vector calculation; 2) there is a reliable capability of ensuring the grid-injected current tracking the grid voltage in phase, owing to the reactive power generated by reactive power equipment is taken into account to control the ES-qZSI’s output current. Simulation and experimental results verify the outstanding features of the proposed AD-PWM and active power control strategy integrated with the reactive power compensation technique for three-phase ES-qZSI PV power system.