The multi-beam echo sounder is usually used in bathymetry activity, the accuracy of temperature, salinity and depth profile data play a very important role in the bathymetry. Unfortunately, those errors among the temperature, salinity and depth data were inevitably brought into the measurement. To analyze the influence of temperature, salinity and depth variations on beam footprint coordinates and quantify its influence value, then, on basis of the indirect measurement data of sound velocity profile, the empirical formula of sound velocity with high precision and strong adaptability were selected to deduce their error formula, and the error value of sound velocity caused by temperature, salinity and depth variation was calculated. On the basis of constant-gradient sound ray tracing model, the horizontal and vertical displacement error formulas of sound wave travel path were derived, and then the influence value of acoustic velocity error on beam footprint coordinates was calculated by combining with sound velocity profile. The experimental results show that temperature has the greatest influence on sound velocity, followed by salinity and depth. The variations of temperature, salinity and depth cause the Z-coordinate variation of the beam footprint to be larger than the X and Y coordinates, up to 0.6% of the depth before the change. The variation of three-dimensional coordinates caused by temperature and salinity decreases with the increase of incident angle, however, the variation of three-dimensional coordinates caused by depth hardly changes with the change of incident angle. The results of this paper can be used for reference to evaluate the accuracy of multi-beam bathymetry with temperature, salinity and depth error.