Shipborne wind observations by a coherent Doppler lidar (CDL) have been conducted to study the structure of the marine atmospheric boundary layer (MABL) during the 2014 Yellow Sea campaign. This paper evaluates uncertainties associated with the ship motion and presents the correction methodology regarding lidar velocity measurement based on modified 4-Doppler beam swing (DBS) solution. The errors of calibrated measurement, both for the anchored and the cruising shipborne observations, are comparable to those of ground-based measurements. The comparison between the lidar and radiosonde results in a bias of −0.23 ms⁻¹ and a standard deviation of 0.87 ms⁻¹ for the wind speed measurement, and 2.48, 8.84° for the wind direction. The biases of horizontal wind speed and random errors of vertical velocity are also estimated using the error propagation theory and frequency spectrum analysis, respectively. The results show that the biases are mainly related to the measuring error of the ship velocity and lidar pointing error, and the random errors are mainly determined by the signal-to-noise ratio (SNR) of the lidar backscattering spectrum signal. It allows for the retrieval of vertical wind, based on one measurement, with random error below 0.15 ms⁻¹ for an appropriate SNR threshold and bias below 0.02 ms⁻¹. The combination of the CDL attitude correction system and the accurate motion correction process has the potential of continuous long-term high temporal and spatial resolution measurement for the MABL thermodynamic and turbulence process.