Hydraulic connections between aquifers is usually studied through hydrochemical analysis or by pumping tests. However, hydrochemical analyses are usually conducted in areas of variable lithology. In addition, the hydrogeological data obtained by drilling and pumping tests are typically insufficient to get 3D distributions of hydraulic head. In this paper, the time-lapse transient electromagnetic method (TEM) is used to image groundwater migration between aquifers in Inner Mongolia, China. First, 1D geophysical models of aquifers are generalized according to the hydrogeological conditions of the region, and the feasibility of detecting the multiple aquifers by TEM is analyzed and discussed. Then, the 2D models of aquifers pre- and post- pumping test are established based on the distribution of groundwater in the aquifers, and the variation law of induced electromotive force measured on the surface is analyzed. The simulation results show that significant time-lapse electromagnetic anomalies can be observed between pre- and post- pumping test and the variation in the induced electromotive force reaches a distinguishable level between 0.7 ms and 100 ms due to the vertical change in the aquifer properties. Furthermore, the electromagnetic variation generated by hydraulic connection between aquifers is greater than 30% within the range of 3/4 of the transmitting loop. Finally, a successful case history to map hydraulic connections between aquifers is conducted using a time-lapse TEM pre- and post- a pumping experiment. This simulation and field experiment shows that time-lapse TEM could characterize and monitor the groundwater migration more effectively than pump tests or hydrogeochemical methods alone.