In this paper, a micro-deformation monitoring method based on Beidou pseudo-satellite system is designed, which can monitor the micro-deformation of buildings with high precision. Because the three-dimensional position change of the monitoring point can reflect the deformation occurring at the monitoring point, after the Beidou pseudo-satellite system is set up, the receiver is placed at the monitoring point, and the deformation of the monitoring point is judged by the change of the positioning result of the receiver. In order to verify the effectiveness of the designed Beidou pseudo-satellite system, we conducted a set of experiments to evaluate it. The experimental results show that the Beidou pseudo-satellite system designed in this paper has higher monitoring accuracy and better stability than the traditional GNSS system monitoring, and the three-dimensional monitoring accuracy is 0.0011m, 0.0007m and 0.0024mrespectively. At the same time, compared with the traditional use of the total station instrument and laser measurement method, Beidou pseudo-satellite system can print out the monitoring results in real time, so it is easier to judge the deformation of the building to prevent the occurrence of danger.