C# and Matlab for the design of lidar echo data acquisition and inversion software were presented. With friendly user interface, C# was used to call the DLL format shared library compiled by function files written in Matlab. The existing atmospheric lidar echo data were applied as an example and the processing results show that this method can improve computing speed and programming efficiency. The software system can be effectively used in the data acquisition and system monitoring. Echo data were preprocessed efficiently with high precision. The retrieving extinction coefficient and echo energy accumulation were processed and displayed dynamically in real time. By adjusting algorithm parameters, it can also be used for other kind of lidar signal processing systems.