At present, most of the smart devices in service for power systems in China use Global Positioning System (GPS) as a clock source, and the synchronization of the micro Phasor Measurement Unit (μPMU) in a distribution network is related to the accuracy of the clock source. With the completion of the Beidou System (BDS), equipments installed with Beidou will gradually become mainstream. First, the influence mechanism of clock pulse accuracy, transformer performance, frequency fluctuation, and harmonic distortion on the measurement error of μPMU is analyzed comprehensively in this paper. Then, the phase angle error of a μPMU measurement device based on BDS is calculated, and the error of the maximum likelihood estimation based on tracking frequency algorithms is analyzed to give the comprehensive error of μPMU under different phasor estimation methods. Finally, the comprehensive errors caused by the clock source, signal conversion, frequency change, harmonic interference, and other factors, are studied. The relevant methods are also used to reduce measurement error. The conclusion will provide theoretical and practical guidance for the large-scale placement of μPMU in distribution networks. This work is supported by the National Natural Science Foundation of China (No. 51977030) and Project of State Grid Eastern Inner Mongolia Electric Power Co., Ltd. (No. SGMDHBOOFCJS1800881).