Three-dimensional hydro-acoustic imaging is a research hot spot in the underwater acoustic signal processing field, which has a wide range of application prospects in marine environmental resource surveying, seabed topography and geomorphological mapping, and underwater early warning and monitoring. To solve the problem that the resolution of the current imaging sonar reduces rapidly with increase in distance and a scanning gap exists in side-scan sonar, we designed a down-looking 3D-imaging sonar with a linear array structure. The imaging scheme adopts a time-domain spatial beam-forming method with the Back Projection (BP) algorithm as the core, and the formation of a virtual plane array can effectively improve the along-track resolution. To cope with the interference of the carrier motion error on the imaging, we proposed a high-precision sub-wavelength motion compensation method based on a real-time acoustic calibration system. Simulation and real data experiments show that the motion compensation method can effectively eliminate the influence of motion error and make the imaging energy more focused, leading to higher-quality acoustic images. Under equal average energy, the maximum superimposed sound intensity values in the imaging results increased by 20.75 dB and 6.57 dB, respectively, for simulation and real data. After motion compensation, the resolution of this imaging system reached 3 cm × 3 cm × 2.5 cm @ Depth = 17 m, TBP = 30 s · Hz.