The invention relates to an intelligent data acquisition method and a system used for space-based laser altimetry. The intelligent data acquisition method of the invention can control and conduct abnormal handling on the data acquisition process, complete accurate and synchronous dual-channel high-speed data acquisition and realize real-time high-capacity intelligent data storage. The intelligent data acquisition system of the invention mainly comprises a signal conditioning unit, a signal transfer switch, an analog-to-digital conversion unit, a data cache unit and a data and control unit; wherein, the dual channels respectively receive emission waves and echoes of a laser altimeter. The invention is characterized by compact system structure, small volume, stable and reliable circuit, large detected dynamic range, little analog-to-digital conversion error, high accuracy and robustness, capability of stably working for a long time without a break, capability of acquiring, transferring and storing all the useful data in real time, capability of adding the radar detection function to the space-based laser altimeter and capability of obtaining surface elevation distribution within the range of light spots and reflectivity.