Experimental research is performed on two-phase flow boiling heat transfer in micro-channels. FC-72 is used as the working fluid. In order to analyze the heat transfer mechanism during two-phase flow boiling, the dimensionless parameters, e.g., boiling number and convection number, are used, and the effect of these parameters on the heat transfer can be confirmed during flow boiling in the micro-channel. In addition, the transition criterion from bubbly/slug flow to annular flow is proposed from the modified Weber number. Based on the boiling heat transfer mechanism obtained from the experiments, a new correlation is proposed to predict the heat transfer coefficient. The new correlation predicts well the experimental results within a mean absolute error of 5.2%.