To provide a microchip inspection system detecting a flow rate in a channel highly accurately with high reliability.

This microchip inspection system comprises: a pump for injecting fluid from the channel into a microchip; a thermal flow rate sensor equipped with a heating resister and a temperature detection member arranged along the fluid channel for outputting a signal corresponding to the flow rate of the fluid; a first flow rate calculation means for calculating the flow rate based on an output from the thermal flow rate sensor; a fluid detection means for detecting existence of the fluid on prescribed two spots in the channel, and outputting a detection signal; a second flow rate calculation means for calculating a calibrated flow rate, based on the detection signal acquired from the fluid detection means; a correction coefficient calculation means for calculating a correction coefficient, based on the calibrated flow rate calculated by the second flow rate calculation means and the flow rate calculated by the first flow rate calculation means; and a correction coefficient table for storing the correction coefficient.