Water migration and methane desorption characteristics directly affect the performance of coalbed methane wells. In this paper, migration and desorption variability of methane and water in adsorption pores, seepage pores, and fractures were studied by laboratory simulation using an improved nuclear magnetic resonance displacement device. The results are as follows: Both adsorbed and bulk methane decreased logarithmically with the increase of the desorption time under the condition of one-stop desorption. The desorption process can be divided into the early rapid decline stage and the later slow desorption stage. In comparison to one-stop desorption, step-by-step depressurizing desorption can effectively increase the loss rate of the methane amount. For the two desorption modes, the variation rate of bulk methane is much higher than that of adsorbed methane at the same desorption time. The sensitivity of large pores to displacement nitrogen pressure is stronger than that of adsorption pores. In the process of methane displacement by water, the variation of bulk methane is larger than that of adsorbed methane, whereas the variation of adsorbed methane is more sensitive to injecting water pressure than that of bulk methane. The above results indicate that the quantity of water injected into the coal seam and the water drainage rate have an effect on methane desorption in the adsorption pore. Therefore, the parameters of depressurization value should be fully considered in the drainage system setting of coalbed methane wells.