A femtosecond laser multimodality molecular imaging system includes a near-infrared pulse generation device for providing near-infrared pulses with a central wavelength of 1010 nm to 1100 nm and a spectral width of less than 25 nm. The near-infrared pulses can excite an optical medium with strong nonlinearity to generate the femtosecond laser pulses with ultra-wide spectrum. A pulse measurement compression and control module measures and compensates the accumulated dispersion of the femtosecond laser pulses arriving at the tissue sample, so as to eliminate the “time domain broadening” effect as much as possible. The obtained shortest pulses can interact with the tissue sample to generate spectral signals from different modalities, thus providing a variety of nonlinear molecular image modalities.