In this paper, a new type ion source based on atmospheric pressure MPT coupled with a simple mass spectrometer is used to obtain protonated molecular ions, molecular ions, and fragment ions of the analytes by adjusting the desorption distance, desorption time, and microwave power. After the discussion of the structures and the MEISD mechanism of the obtained ions, the probable gas-phase reaction in MPT ion source is described. By comparison of the full-scan spectra obtained by the present method with the MSn results obtained by MPT-LTQ MS, the accuracy of the present method is proven. The developed MPTDI-TOF-MS is expected to facilitate the qualitative and quantitative analysis of complex samples instead of using an expensive tandem mass spectrometer.