With the development of instrumental miniaturization, the portable mass spectrometer is becoming a new tool for on-site rapid analysis of environmental samples. Membrane inlet (MI) and photoionization (PI) are two commonly used sampling and ionization techniques, respectively, as they both exhibit detection selectivity for volatile organic compounds (VOCs). In this paper, a membrane inlet photoionization ion trap mass spectrometer was developed for the direct analysis of VOCs in gaseous samples. With the new structure and timing design, various operation modes were proposed and tested. In particular, the use of pulse carrier gas can integrate the appropriate pressure conditions required by each module, thus improving the efficiency of analyte transport, ionization, and mass analysis. The detection limit of sub-ppb was obtained, and the response time can be greatly reduced by increasing the sample flow rate. Furthermore, the capability of selective enrichment for organic analytes was also realized by using a special accumulation mode with a modified sequence, which is easy to operate because no additional devices are needed.