For the current solar charging controller’s insufficient protection to the battery, the battery’s life span is shortened, a kind of solar charging controller program based on Atmega16 is researched. Atmega16 with low-power and high performance is used as the core device to control the entire circuit. System hardware circuit consists of solar battery charging circuits, voltage acquisition and display circuits, single-chip microcomputer control and RS-485 serial communication circuits, which mainly realize the acquisition and display of battery voltage. Software is based on pulse width modulation (PWM) strategy, PWM control signal is outputted from single-chip microcomputer through programming. The control of turning on and off for power switching device metal oxide semiconductor (MOS) tube is realized by the control signal so as to control charging battery through solar plate. According to the requirements of the controller, software program is programmed and battery charging efficiency is realized by the software, which makes the battery no in overcharge and over discharge state. So the battery is protected and the service life of the battery is prolonged.