Spatial microgravity is a significant factor affecting and causing physiological changes of organisms in space environment. On-site assessment of the damage associated to microgravity is very important for future long-term space exploration of mankind. In this paper, a new microfluidic device for analyzing the damage of microgravity on Caenorhabditis elegans (C. elegans) has been developed. This device is mainly composed of a microfluidic chip, a dual imaging module, and an imaging acquisition and processing module, which are integrated into a compact system. The microfluidic chip is designed as a platform for monitoring C. elegans, which is captured in an imaging region through a suction structure in the microfluidic chip. A dual imaging module is designed to obtain the images of bright field and fluorescence of C. elegans. The behaviors of C. elegans are analyzed based on the dual-mode imaging of bright field and fluorescence to assess the degree of damage due to microgravity. A comparative study using a commercial microscope is also conducted to demonstrate the unique advantage of the developed system under the simulated microgravity. The results show that the developed system can evaluate the damage of C. elegans under microgravity accurately and conveniently. Furthermore, this device has compact size and weight, easy operation, and low-cost, which could be highly advantageous for on-site evaluation of the damage to microorganisms under microgravity in a space station.