A design method for a low-light level camera driving system based on an autonomous underwater vehicle was proposed. First, the noises of an electron multiplying charge-coupled device camera was analyzed, and the principle and method of designing conventional driving circuits was proposed taking into consideration the relationship between dark current noise and clock-induced charge noise. Next, the issue of power consumption in totem-pole circuits applied to electron multiplying drivers was discussed, and a power optimization plan was presented. A high-precision system clock was used for fine adjustments of the driving signal phase and pulse width and solving the problem of amplitude overlap rate insufficiency. Finally, the low-light level camera structure and experimental results were presented. The experiments indicate that the system-generated conventional driving signal frequency is 10 MHz. The serial transfer clock amplitude overlap rate and parallel transfer clock amplitude overlap rate are better than 50% and 90%, respectively. The phase adjustment accuracy of the driving signal and pulse width adjustment accuracy are 18° and 5 ns, respectively. The driving signal is stable and smooth, the electron multiplying driving signal is highly adjustable, and the power consumption is lowered by 7.2%. The parameters of noise, size, and power consumption were considered in this design. Thus, it can be widely used in underwater low-light level imaging as well as conventional charge-coupled devices.