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The detection of genetically modified (GM) maize events is an inevitable necessity under the strict regulatory systems of many countries. To screen for GM maize events, we developed a multiplex PCR system to specifically detect 29 GM maize events as well as the cauliflower mosaic virus 35S promoter, the Agrobacterium tumefaciens nos terminator, the Streptomyces viridochromogenes pat gene, and the endogenous zSSIIb maize reference gene. These targets were divided into five panels for screening and event-specific detection by multiplex (10-plex, 7-plex, 7-plex, 4-plex, and 5-plex) PCR. All amplification products were separated and visualized by fluorescence capillary electrophoresis (CE). By taking advantage of the high resolution, multiple fluorescence detection, and high sensitivity of CE, our system was able to identify all targets simultaneously with a limit of detection of 0.1%. The accurate identification of specific amplification peaks from different GM maize materials by CE confirmed the specificity of the system. To verify the practical applicability of this system, we analyzed 20 blind samples. We successfully identified five MON810, four TC1507, and three MIR162 samples. The detection of concomitant elements also verified the accuracy of this approach. Our system can, therefore, be used for the screening and detection of GM maize events. The system, which is easy to use, facilitates high-throughput detection with the help of a high-throughput platform and automated identification software. Multiplex PCR coupled with CE is, thus, very suitable for the detection of genetically modified organisms (GMOs) with a large number of detection targets. Additional multiplexed electrophoretic targets can be easily incorporated as well, thereby increasing the usefulness of this system as the number of GMO events continues to increase.