Water-cooled micro channel separate heat pipe (MCSHP) is an efficient cooling technology for data centres. To optimise the design of MCSHP, some numerical models have been proposed. However, the matched air-side and refrigerant side heat transfer correlations of evaporators in these numerical models were suitable to predict the heat transfer performance of separate heat pipe where the Reynolds number is higher than 75; they are unsuited to predict the heat transfer performance of MCSHP under partial load and low airflow rate. In this study, a steady-state numerical model with a combination of ε-NTU methods was developed. The existed air-side heat transfer correlations of louvered fin heat exchanger and refrigerant side two-phase heat transfer correlations of micro channel heat exchanger were tested in the model under different airflow rates with the optimal refrigerant filling ratio. The mean absolute deviation between the selected model and experiment was less than 10%. By using this model, the thermal performance under partial heating load and airflow rate were analysed. The simulation results show that the MCSHP has superior start-up performance to ensure the data centre thermal safety under low airflow rates (200m3/h-1500m3/h) and partial heating load rates (19.2%-51.1%). The developed model can be used to improve the controllability and energy-saving performance of MCSHP.