Rhamnolipid (Rha) is an efficient green surfactant that is able to promote hydrate generation, it can be applied to the hydrate method of separating. However, the effect of rhamnolipid on the separation of methane and nitrogen by the hydrate method is not clear. Therefore, in this paper, we investigated the effect of rhamnolipid on methane hydrate formation and the separation between methane and nitrogen via hydrate method. Firstly, the effects of five concentrations (0 ppm, 200 ppm, 400 ppm, 600 ppm and 800 ppm), temperatures and pressures on methane hydrate formation were studied separately. The rate of methane hydrate formation was positively correlated with experimental pressure. The gas consumption increased rapidly with the rhamnolipid concentration, and then increased slowly to a steady state. The final gas consumption above 200 ppm rhamnolipid concentrations could be increased more than five times compared with pure water conditions. The promotion of methane hydrate production is most pronounced at 274.15 K, mainly depending on the diffusion of gas molecules in solution and the ease of hydrate nucleation. Then, the interfacial tension at different concentrations was measured by the suspension drop method, and the relationship between the interfacial tension and the rate of hydrate formation was studied. Hydrate formation rate shows a multiplicative power function with the interfacial tension. What’s more, the kinetics of hydrate formation and gas separation effect of 3:1 CH4/N2 at 274.15 K and 7 MPa were studied with five concentrations. And 200 ppm was found to be the optimum concentration for separation, the separation factor is 8.25. Finally, the kinetics and thermodynamics of hydrate formation and gas separation effect of 1:1 CH4/N2 at 274.15 K and 9 MPa were also investigated, and the separation factor reached a maximum of 12.7 at 800 ppm, and the methane gas recovery rate also reached the maximum at 40.46%. The results of this study can provide some theoretical guidance for the optimal selection of green surfactants in separation by hydrate method.