The high-sensitivity electron bombarded active pixel sensor (EBAPS) not only has the characteristics of high gain and high sensitivity of vacuum imaging devices, but also has the digital characteristics of solid-state imaging devices, which greatly improves the level of night vision imaging. A natural color low-level-light EBAPS imaging system was built based on three-color liquid crystal tunable filter (LCTF). According to the characteristics of low-level-light images, the color enhancement processing such as grayscale stretching, white balance, and color correction was performed on the color images obtained by the system. The experimental results show that the system can realize the natural low-illumination color imaging that reflects the color characteristics of the scene itself, which can effectively improve the observation effect of the characteristics of the target scene at night, and can realize the color imaging under 5×10^?4 lx illumination.