For meeting the requirements of quickly designing high performance micro-channel heat exchanger, a general three-dimensional simulation approach considering the factors of heat conductions via fins, quality distribution among micro-channel tubes and flexible flow circuit arrangements is proposed in this paper. In the simulation approach, an approximate analytical solution for describing the three-dimensional heat conductions via fins is presented, having higher computation speed over the numerical method of directly calculating heat conductions; a theory-based refrigerant distribution model for predicting the quality distribution among micro-channel tubes is established instead of using homogeneous quality distribution, resulting in the improvement of evaporator model accuracy; and a graph-theory based computation algorithm is developed to calculate any possible flow circuit conveniently and quickly. The presented model is validated by experiments, and the deviations of the predicted heat capacity of micro-channel evaporator, condenser and gas cooler from the measured ones are within ±5%.