Accurate and rapid identification of multiple pathogens simultaneously is paramount for global public health, including the detection of different influenza virus subtypes. Recently, the development of CRISPR/Cas technology and its combination with isothermal amplification technology has presented promising opportunities for exploiting point-of-care, highly sensitive and specific detection methods. However, there have been several challenges in terms of multiplex detection and compatibility with isothermal amplification technology, especially loop-mediated isothermal amplification (LAMP). In this study, we introduced a multiplex detection platform, named spatial encoding of centrifugal microfluidic disc integrated smartphone-controlled platform (SEDphone), which was based on CRISPR/Cas12a and RT/LAMP technology. Five distinct influenza virus subtypes could be simultaneously identified: influenza A virus H1N1, H3N2, H5N1, H7N9, and influenza B virus. The assay limit of detection reached 10 copies/μL within a 45-minute timeframe. Furthermore, the clinical efficacy was validated by detecting 22 positive and 16 negative clinical samples. We anticipate that this simple yet efficient platform holds significant potential as a versatile multiplex pathogen detection in both research and diagnostic settings.