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The invention discloses an imaging method for an endoscope imaging system and the endoscope imaging system. The method comprises the following steps: receiving a mode switching instruction for switching from a first imaging mode to a second imaging mode; in the second imaging mode, the light source host is controlled to alternately output visible light and exciting light, a visible light signal is obtained when the light source host outputs the visible light, and a fluorescence signal is obtained when the light source host outputs the exciting light; the second imaging mode sequentially comprises a first stage and a second stage, in the first stage, a second visible light signal and a first fluorescence signal are acquired, and only a second visible light video image generated based on the second visible light signal is displayed; and in the second stage, acquiring a third visible light signal and a second fluorescence signal, and displaying a fluorescence video image at least based on the second fluorescence signal. According to the invention, jamming in the mode switching process can be avoided.