In order to reduce the energy consumption of data center, the micro channel separate heat pipe (MCSHP) would reduce the airflow rate according to the actual heating load, resulting in a reduce of thermal performance. In order to investigate and analyze the thermal performance of MCSHP under low airflow rate and heating load, a one-dimensional steady-state model was established. Compared with the experimental results, the maximum average relative error of the result predicted by the established model was 6.3%. By using the established model, the effect of operation parameters on the thermal performance of MCSHP and thermal safety of data center were investigated. When the server exhaust air temperature increased from 27 ℃ to 39 ℃, the cooling capacity was increased by more than 60% under the various airflow rates. When chilled water supply temperature increased from 6 ℃ to 18 ℃, the cooling capacity was decreased by a maximum of 41.8%. The cooling capacity and refrigerant mass flow rate increased with the increasing height difference between evaporator and condenser under airflow rate ranged from 200 to 1 400 m3/h，and the growth rate of cooling capacity increased with the airflow rate. However, the growth rate of cooling capacity decreased with the height difference under the same airflow rate. Those results give a guidance to improve the design optimization and energy-saving operation of the application of MCSHP in data center.