A model of wax deposition based on molecular diffusion mechanism, for oil-gas two-phase stratified pipe flow is developed. In the model, unidirectional fully developed flow analyses of momentum, heat and mass transfer are presented. And, a cube cage model is used to describe the wax deposit structure considering the effect of oil flow shear on the deposit. Calculation of wax deposit is compared well with a flow loop experiment. In particular, the model could give the wax deposit forming a crescent shape at the cross section of pipe, which is observed in different experiments. Furthermore, the cause of forming a crescent shape is revealed, which is indicated by the non-uniform circumferential distribution of mass flux for wax deposition along the pipe wall wetted by the oil. The mass flux from oil bulk flow to the oil-deposit interface is closely related to three parameters, diffusivity at oil-deposit interface, the temperature gradient at the oil-deposit interface at different time, and the slope of the wax solubility curve at oil-deposit interface temperature.