The invention discloses an electron beam excitation fluorescence large-range direct detection imaging apparatus and a method thereof. The imaging apparatus comprises a scanning electron microscope system, a scanning signal generator, a fluorescence collection coupling system, a semiconductor photodetector, a scanning synchronization signal collector and a synergic control and data processing output system. According to the present invention, by using the modular architecture, the configuration adjustment and the subsequent upgrade of each module are flexible and convenient; and by introducingthe large-area semiconductor photoelectric detection chip of the semiconductor photodetector, the fluorescence excited by the scanning electron microscope system in the large imaging visual field range can be concentrated and coupled to the semiconductor photodetector at the same high collection efficiency, such that the problem that the fluorescence excitation intensities or the fluorescence excitation yields at different positions of the image obtained through the large-range fluorescence scanning imaging are difficultly calculated and compared by using the standard is solved so as to complete the large-range rapid detection and analysis based on the electron beam excitation fluorescence signals.