Sequential switching shunt regulator (S3R) has been widely used in satellites for its simple structure and high reliability. Double section functioning, which has two sections operating simultaneously, is the other operating mode of S3R beside the normal mode. It is inevitable and can lead to larger bus voltage ripple, less controllability and higher switching losses. A detailed analysis based on the double section functioning process description is given on the boundary load current, the main bus voltage ripple and the switching frequency. Considering the influence of double section functioning, a new method of control loop design of S3R is proposed based on the small single mathematical model. A 4.5 kW S3R prototype is built to verify the control loop design, and the load region of double section functioning can be limited as designed.