In order to solve the problem of online calibration of angle measuring system, we propose a self-calibration method based on multi-head layout. Through the measurement data of multiple sets of sensors, the relationship between the measured value and the error is established with the properties of circle closure and Fourier series. Based on the principle of multi-reading head, the self-calibration reading head layout is optimized to suppress the error and achieve a single reading head self-calibration sensor. To carry out a test verification, we design a one axis turntable. The experimental results show that the angular error of the sensor is 6.10″ with the proposed self-calibration method. In the same measurement environment, the calibration accuracy is close to the traditional harmonic calibration method with external reference. It is proved that self-calibration method can effectively suppress the angle error and improve the measurement accuracy.