Multispectral full-waveform lidar can simultaneously acquire full-waveform comprehensive information including implicit spectrum information. Waveform decomposition is a key technology that affects the accuracy of multiple echo parameter inversion. A waveform decomposition method suitable for multispectral lidar data was proposed, which flexibly selected fitting sub-functions for each channel and made full use of the spatial correlation between multiple channels to achieve accurate extraction of the spatial position and spectral information of the target; the mapping relationship between the spectral space and the RGB color space was established to achieve the target three-dimensional color reconstruction. Experimental test results show that this method can achieve full-time 3D color reconstruction of the target, effectively overcome the influence of weak echo signal loss and ambient light interference, and effectively improve the accuracy of target ranging and color information inversion. The experimental results show that the method effectively overcomes the interference of ambient light and can achieve the target three-dimensional color reconstruction throughout the day. By comparing with existing methods, the two error evaluation indexes of error standard deviation and determination coefficient R2 both verify that the proposed method has higher ranging accuracy and color information inversion accuracy. In addition, the experimental results verify that the optimal pulse accumulation number can effectively balance the data processing accuracy and scanning efficiency. In the future, the proposed method can be extended to other lidar systems to further improve the accuracy of target 3D color reconstruction by optimizing the laser detection bands.