An unsteady numerical heat transfer model was proposed to study the operation stability and heat-affected radius of medium-deep borehole heat exchanger (MDBHE). The governing equations were discretized and solved based on the finite difference method (FDM). The numerical results were verified through the measured data of a project. On this basis, the outlet water temperature of MDBHE and the temperature of rock and soil under long-term operation were studied. The sensitivity analysis of the operating parameters affecting the thermal disturbance of MDBHE was also carried out. Results show that after operation of 15 years, the outlet temperature of MDBHE was relatively stable, and the outlet temperature of MDBHE was basically in a quasi-steady state from the 11th year, and the maximum temperature drop ratio of the surrounding rock and soil was only 6.5%. With the increase in the thermal diffusivity of rock and soil, the increase rate of heat-affected radius of MDBHE was faster in the early stage and slower in the later stage. When the thermal diffusivity a increased from 1.43×10^-6 m²/s to 2.01×10^-6 m²/s, the heat-affected radius r increased from 82.69 m to 99.23 m, with an increase rate of 20%. The relationship between them changed exponentially and satisfied the equation r=-151.99×exp[-a/(5.14×10^-7)]+98.14, where R²=0.97. This research has certain reference significance for the design of MDBHE.