A lidar three-dimensional imaging system based on a virtual instrument comprises a three-dimensional scene modeling module, a lidar testing system simulation environment modeling module, a full-waveform signal processing module and a three-dimensional reconstruction module. The three-dimensional scene modeling module comprises a three-dimensional model loading element used for setting background colors, visual angle control, illumination, a projection mode, a display model and other basic scene projects. The lidar testing system simulation environment modeling module comprises four modeling sub-modules which are a laser pulse model, an atmospheric transmission model, an object interaction model and a receiving unit model. The laser pulse model is used for simulating a laser source according to the wavelength, pulse width, energy and other characteristics of a laser. The atmospheric transmission model is used for simulating a tested atmospheric environment, so that a noise model is generated for acting on the laser. The object interaction model is used for simulating effects of the laser and a detected object, and the effects comprise mirror reflection, diffuse reflection, surface reflection and speckles. The receiving unit model is used for simulating detector noise and amplifier noise which are generated after sensing.