A femtosecond laser multimodality molecular imaging system, comprising a supercontinuum generation module, a pulse measurement, compression and control module and an optical microscope module; the supercontinuum generation module comprises a near-infrared pulse generation device, and an optical medium with strong nonlinearity; the near-infrared pulse generation device is configured to provide near-infrared pulses having a center wavelength of 1010 nm to 1100 nm, and a spectral width of less than 25 nm; the optical medium with strong nonlinearity is configured to be excited by the near-infrared pulses to generate femtosecond laser pulses; the pulse measurement, compression and control module comprises a first optical component and a measurement module; the first optical component is configured to receive the femtosecond laser pulses; the measurement module is configured to measure a dispersion in an optical path of a system, adjust parameters of the first optical component to perform dispersion compensation on the femtosecond laser pulses according to a measurement result, and obtain compressed femtosecond laser pulses; and the optical microscope module comprises a second optical component, a sample stage and a first signal acquisition device; wherein the sample stage is configured to receive on it a tissue sample and is placed at a position suitable for the compressed femtosecond laser pulses, after passing through the second optical component, to interact with a tissue sample on the sample stage to generate multimodality signals; and the first signal acquisition device is configured to collect the multimodality signals characterized in that the second optical component comprises a first mirror, a scanning galvanometer module, a second mirror, a dichroic mirror, an optical microscope objective and a plurality of filters (F1, F2,..., F(n-1)), the first signal acquisition device comprises a plurality of photodetectors (PMT1, PMT2,..., PMT(n-1)) corresponding to the plurality of filters (F1, F2,..., F(n-1)), and the plurality of photodetectors are connected to a control device; wherein the sample stage is at a position where the compressed femtosecond laser pulses are focused after passing through the first mirror into the scanning galvanometer module; and the dichroic mirror is configured to reflect the multimodality signals, the plurality of filters (F1, F2,..., F(n-1)) is configured to separate the multimodality signals, the plurality of photodetectors (PMT1, PMT2,..., PMT(n-1)) is configured to collect the multimodality signals and the control device is configured to receive the multimodality signals. the supercontinuum generation module comprises a near-infrared pulse generation device, and an optical medium with strong nonlinearity; the near-infrared pulse generation device is configured to provide near-infrared pulses having a center wavelength of 1010 nm to 1100 nm, and a spectral width of less than 25 nm; the optical medium with strong nonlinearity is configured to be excited by the near-infrared pulses to generate femtosecond laser pulses; the pulse measurement, compression and control module comprises a first optical component and a measurement module; the first optical component is configured to receive the femtosecond laser pulses; the measurement module is configured to measure a dispersion in an optical path of a system, adjust parameters of the first optical component to perform dispersion compensation on the femtosecond laser pulses according to a measurement result, and obtain compressed femtosecond laser pulses; and the optical microscope module comprises a second optical component, a sample stage and a first signal acquisition device; wherein the sample stage is configured to receive on it a tissue sample and is placed at a position suitable for the compressed femtosecond laser pulses, after passing through the second optical component, to interact with a tissue sample on the sample stage to generate multimodality signals; and the first signal acquisition device is configured to collect the multimodality signals characterized in that the second optical component comprises a first mirror, a scanning galvanometer module, a second mirror, a dichroic mirror, an optical microscope objective and a plurality of filters (F1, F2,..., F(n-1)), the first signal acquisition device comprises a plurality of photodetectors (PMT1, PMT2,..., PMT(n-1)) corresponding to the plurality of filters (F1, F2,..., F(n-1)), and the plurality of photodetectors are connected to a control device; wherein the sample stage is at a position where the compressed femtosecond laser pulses are focused after passing through the first mirror into the scanning galvanometer module; and the dichroic mirror is configured to reflect the multimodality signals, the plurality of filters (F1, F2,..., F(n-1)) is configured to separate the multimodality signals, the plurality of photodetectors (PMT1, PMT2,..., PMT(n-1)) is configured to collect the multimodality signals and the control device is configured to receive the multimodality signals.