Comparing to the single aperture imaging system, Artificial Compound-Eyes (ACE) imaging system has some nice features, such as small size and stereo vision. This paper introduces our multiple-focus ACE imaging system. The system mainly consists of (a) a micro-lens array fabricated by Micro-Electro-Mechanical-System (MEMS) technology, (b) a CMOS chip, (c) a 3D mechanical moving stage, and (d) an auto-focus software module. It can simultaneously observe the object by several channels with different focus, therefore the focal length of the system can be adjusted by selecting different channels. Besides, a software module is developed to carry out auto-focus. The system is applicable to the fields of industry inspection, bio-medical imaging and robot vision.