The invention discloses a hardware and software cooperation method for measuring cloud layer height and thickness. The method comprises the following steps: automatic emission and automatic collection of a high speed laser pulse train are realized, and collected discrete data are stored in an FPGA and then processed via an embedded processor. According to the hardware and software cooperation method, the high speed FPGA is used for pulse emission and data collection, speed higher than that of other hardware systems can be realized, and off-chip resources can be saved. According to the hardware and software cooperation method, a curvature segmentation and wavelet filtering method is adopted and is greater than a single value calculating method in terms of real-time performance, flexibility and measuring precision. Compared with the prior art, a high speed FPGA-based cloud layer height and thickness measuring instrument is advantaged by high speed, strong processing performance, monolithic integration, no need for redundant peripheral chips, capability of making it convenient to make an SOPC and realize chunked transplant, application to continuous, wireless and remote measurement, and wide application to the various fields such as meteorology, civilian use, transportation and the like.