Nuclear Magnetic Resonance (NMR) is one of the most powerful analytical tools nowadays, with wide applications in the fields of chemistry, biology and medicine. The spatial encoding ultrafast method proposed by Frydman et al. in 2002 greatly enhanced the sampling efficiency of multi-dimensional NMR spectroscopy. One problem with the Frydman’s method is that it is difficult to selectively detect multiple resonances at non-continuous discrete frequencies, due to the fast-switching bipolar gradients that are required for spatial encoding. In this study, we proposed a novel selective spatial encoding ultrafast method, aiming to solve two problems often encountered when utilizing the Frydman’s method in practical chemical and biological applications. The first problem is to detect weak signals in the presence of strong signals with limited dynamic range; and the second problem is to detect the signals of interests (e.g., peaks from labeled nuclei) exclusively with the rest of resonances in the background unexcited. The proposed method utilized a selective pulse to destroy the encoding process selectively, such that selective suppression of strong peaks or excitation of non-continuous discrete frequency points of interest could be achieved. We also showed that only the spectral peak selected by the selective pulse would remain if the selective inverse pulse was replaced by a hard inverse pulse. The feasibility and validity of this method were demonstrated by both theoretical analyses and experiments.