A set of 4000-meter laser Doppler hydrothermal velocity measurement prototype suitable for deep sea in-situ measurement is developed in this work. In the system, an integrated design is adopted. The system is composed of a light source module, an optical module, and a Doppler signal processing module. The system is encapsulated in a pressure chamber with L500 mm × Φ205 mm to form an integrated optical measuring probe. An optical path of two-beam laser Doppler velocity measurement with strong local oscillator is proposed. The prototype is used to measure the simulated velocity in the laboratory. The measurement range is 0.01–10 m/s, and the flow velocity measurement resolution is 0.001 m/s. The experimental results preliminarily prove the feasibility of the laser Doppler velocity measurement system. After that, a withstanding voltage test on the system is conducted at the Qingdao Deep Sea Base, and the system obtains a normal signal under a high pressure of 40 MPa. A speed comparison measurement is carried out at the China Institute of Water Resources and Hydropower Research. In a low speed range from 0.01 m/s to 0.2 m/s, comparing with the acoustic Doppler velocity meter, the maximum measurement relative error is –9.43%. In a high speed range from 0.8 m/s to 9.6 m/s, comparing with the nozzle standard flow rate system, the maximum relative measurement error is –1.65%. The prototype system is tested in a shallow sea in Lingshui, Hainan. The sinking speed of the prototype system that sinks together with a crane down to a water depth of 50 m, and the towing speed of the system together with the ship at a depth of 2 m are tested. The test proves that the prototype system works normally in a shallow sea environment.