Micro-channel separated heat pipes (micro-channel SHPs), which may cycle without inputting additional electrical power, have shown their advantages of energy saving and compact structure, and they are preferred in the cooling of electronic equipment with narrow inner space. The non-uniformly distributed refrigerant flow among multiple flat tubes and air flow among multiple fins of micro-channel heat exchangers may have a significant effect on the performance of SHPs. In this study, a quasi-three-dimensional distributed parameter model of micro-channel SHPs is proposed for predicting the effects of non-uniformly distributed refrigerant and air flows on the performance. The model is developed by modeling all the components of a micro-channel SHP, i.e. an evaporator, an ascending tube, a condenser and a descending tube, respectively. In the model, the refrigerant flow is described as uneven flow among tubes and the flow direction is fixed inside each tube; the air flow is modelled as the flow with two-dimensional uneven distribution at the windward of heat exchanger and with the fixed direction across the heat exchanger; the three-dimensional partition method is applied to the control volume partition of flat tubes and fins. The proposed model is validated by experiments, and the results show that the deviations between simulated and experimental data of the heat transfer capacity, the temperature difference of micro-channel SHP, the outlet air temperature of evaporator and the outlet air temperature of condenser are 4.6%, 0.9 °C, 1.1 °C and 0.4 °C, respectively.