The invention discloses an electron beam excitation fluorescence imaging and fluorescence spectrum measurement apparatus and a method thereof. The electron beam excitation fluorescence imaging and fluorescence spectrum measurement apparatus comprises a scanning electron microscope system, a scanning signal generator, a fluorescence collection coupling transmission system, a fluorescence intensitydetector, a fluorescence spectrum detector, a scanning synchronization signal collector and a cooperative control and data processing output system. According to the present invention, by using the modular framework, the configuration adjustment and the subsequent upgrading of each module are flexible and convenient; various modules cooperatively work under the unified synchronization and coordination control of the collaborative control and data processing output system so as to ensure the strict timing and the strict logical sequence, and the operation conditions of each module can be detected by feeding back the interactive signals so as to finally achieve the high-precision electron beam excitation fluorescence imaging and fluorescence spectrum measurement; and with the fluorescence collection coupling transmission system and the fluorescence spectrum detector, the resolution of the scanning electron microscope is substantially improved.