When the CNC machining centers using the laser tool setting instrument to measure the corner radius of end mill, there are still systematic errors even after precision adjustment and calibration. The principle of measuring the corner radius of end mill with laser tool setting instrument was analyzed,it was pointed out that the laser shielding error was the main factor of this system error; an error compensation formula for the laser shielding error was established and verified by experiment. The results show that the measurement error is reduced from 0.08 mm to 0.02 mm after compensation, which proves the practicability of this compensation method.