The resolving power of the drift tube ion mobility spectrometry (IMS) is mainly dependent on the drift length, the drift voltage, the pulse width of an ion gate, and the pressure inside the drift tube. Electrospray ionization (ESI)-IMS is a highly sensitive and reliable technique for the detection and analysis of nonvolatile compounds, and high resolving power is necessary to separate structurally similar compounds. To improve the analytical performance of atmospheric pressure ESI-IMS, the Fourier deconvolution (FD) multiplexing technique is investigated as an effective and convenient means to improve the resolving power as well as the signal-to-noise ratio. By reducing the equivalent ion gate opening width to 5 μs using a typical Tyndall-Powell ion shutter, a high resolving power RP up to 170 can be achieved with a drift length of 12 cm and a drift voltage of 10 kV. Rhodamine 6G (R6G), sodium dodecyl sulfate (SDS), methacycline, oxytetracycline, and ractopamine were evaluated using the FD-ESI-IMS, and mixtures with similar ion mobility can be well separated without prolonging the drift length.