We have developed a fluorescence optical detection system using a digital micromirror device (DMD) for monitoring 3D cell culture matrices in situ. Full 3D imaging with fast scanning speed was implemented by the combined action of a DMD and a motorized stage. Imaging results with fluorescent microbeads measure the minimum axial resolution of the system as $6.3{mu}m$, while full 1-mm scanning through 3D alginate-based matrix was demonstrated. For cell imaging, improved images were obtained by removing background fluorescence although the scanning distance was reduced because of low intracellular fluorescence efficiency. The system is expected to be useful to study various dynamics and behaviors of 3-dimensionally cultured cells in microfluidic systems.