It is difficult to explore the overlapping double-layer waterlogged goafs using the transient electromagnetic method. The reason is that upper waterlogged goafs will hinder the propagation of the electromagnetic field, thus prolonging the observation of the lower waterlogged goafs and reducing the signal-to-noise ratio. Besides, the burial depths and layer spacings of double-layer waterlogged goafs affect the signal-to-noise ratio and the observation time of transient electromagnetic signals. By building a double-layer waterlogged goaf model based on the Majiayan coal mine in Shanxi, this study analyzed the electromagnetic field propagation under layer spacings of 25 m, 50 m, 75 m, and 100 m,and calculated the observation time of waterlogged goafs with different layer spacings. Furthermore, it quantitatively characterized the differences between induced voltages in the double-layer waterlogged goafs with different layer spacings using root mean square errors. Additionally, this study proposed the identification criteria for explorable lower waterlogged goafs based on the record errors and noise levels during the observation. The results of physical simulation experiments are as follows: The differences between the induced voltages of double-layered waterlogged goafs with different layer spacings occur mainly in the late stage; the differences between induced voltages gradually decrease as the layer spacing and the burial depth of upper waterlogged goafs increases; the difference between induced voltages is close to the noise level when the layer spacing is greater than 75 m. The actual detection of the double layer waterlogged goaf with a spacing of 75 meters was conducted in Majiayan Coal Mine, and the results showed that the lower waterlogged goaf was not effectively identified.Therefore, It is difficult to effectively explore the lower waterlogged goafs when the layer spacing is greater than 75 m.