To ensure safety for a handling robot used in polymer microfluidic chip, a reliability design was presented by researching the collision protection between handling robot and objects around. A collision protection system mainly based on a relay and a electromagnetic brake was designed to distinguish collision signal and to complete protection for handling robot immediately. The position precision of the handling robot caused by the collision protection system was calculated and analyzed. The experimental results indicate that the inertial displacement can be controlled to less than 1 mm and the collision protection system has no affect on position precision. These results means that designed system is beneficial to reliability and automation of the microfluidic chip automated fabrication system.