The standalone power supply system, based on the two-stage three-phase four-leg matrix converter, is able to provide balanced voltages for unbalanced or nonlinear loads. To improve the quality of output voltages under wide input range, three different modulation patterns of conversion stage are used for specified input conditions, and a pattern-selection strategy based on a judgment function is proposed. On the output of the converter is a three-phase four-wire LC filter, and a filter-state feedback algorithm is proposed to place poles and decouple the interference between three-phase voltages caused by neutral inductor. Based on decoupled model, proportional resonant controller of output voltage in three-phase static reference frame is established. The validity and feasibility of the proposed modulation strategy and decoupling algorithm is verified by both simulation and experimental results.