The performance of an ultra-short baseline (USBL) positioning system is limited by noises and errors from physical environment and other sources. One of the major errors in USBL positioning is to neglect the sensor misalignment which produces static yaw, pitch, and roll offsets. In this study, a circular survey observation scheme is first proposed to study the positioning errors of a USBL system with a fixed seabed transponder. The center of the circular survey scheme is assumed to be located over the top of the transponder. Mathematical equations of the transponder positioning with yaw, pitch, and roll offsets are derived, respectively. According to characteristics of positioning errors arose from yaw, pitch, and roll offsets, an iterative procedure of first getting roll offset, next computing yaw offset, and then obtaining pitch offset for sensor misalignment correction is established. Simulation results indicate that the iterative procedure can effectively obtain all offsets with high determination accuracy and the computation can rapidly converge to desired error tolerance in a few iterations. However, the center of circular vessel survey scheme is almost impossible to be exactly located over the top of the transponder. In such a case, the horizontal positioning error resulting from pitch offset or roll offset is no more a circle function. As a result, it will fail to evaluate the angle offsets through above iterative procedure unless the deviation from real and estimate horizontal transponder position is extremely small comparing to the transponder depth. Therefore, in addition to circular survey scheme, this study proposed a straight survey scheme to study the patterns of positioning error resulting from yaw, pitch, and roll offsets. Similar to the philosophy of establishing the iterative procedure described above, the iterative procedure of first getting pitch offset, next computing roll offset, and then obtaining yaw offset for sensor misalignment correction is established. Again, simulation results show that the iterative procedure can find all offsets with high determination accuracy and has the advantage of quick converging. Besides, the iterative procedure can still obtain correct angle offsets even though there is a constant heading deviation from the direction of the straight vessel track during vessel survey.