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Infrared (IR) sensors are widely used on robotics platforms for measurement purposes. Low-cost small unmanned aerial vehicles (UAVs) have drawn broad interests during recent years for their various uses in many applications. This paper introduces a two-stage IR sensor calibration method for the attitude estimation of low-cost UAVs. The first stage is based on ground and flight tuning procedures, which are concluded from experience; the second stage is to use the calibration algorithm with inertial measurement unit (IMU) as the baseline reference. The implementation and optimization of the proposed algorithm is described and explained in detail. The experimental flight results are compared and discussed in the end.