A novel digital controller solution was proposed, according to the actual driving of PV pumping system. To reduce freewheeling power consumption, MOSFET was used as freewheeling current path instead of diode based on synchronous rectification, which was helpful to reduce temperature of the controller and to improve the system reliability. The deadbeat digital controller was designed based on adaptive UKF, to identify and modify system parameters on line. Simulation and experimental results show that the designed scheme is easy to digital implementation, valid for parameters identification, and has higher current control precision. Therefore, it is effective to improve the performance of PV pumping system.