The novelty of this paper is to numerically investigate the effect of manufacturing error and misalignment on the transient lubrication behavior of dynamically loaded journal bearings with micro-groove. Based on the average Reynolds equation considering the mass conservation cavitation algorithm, the asperity contact model, and the force balance equation, the mixed lubrication model under time-varying dynamic loads is developed. Meanwhile, mathematical functions are given for the bearings with different surface profiles, including the circumferential and axial manufacturing errors of the bearing, the horizontal and vertical deflection angles of the journal, and the micro-grooves with different distribution forms. According to this model, the lubrication characteristics of the bearing are systematically investigated at different horizontal and vertical deflection angles, amplitudes, spatial numbers, and phase angles of the circumferential waviness, as well as shape profiles of the axial error. In addition, the performance parameters of dynamically loaded journal bearings with ideal and actual surfaces under different micro-groove distributions are comparatively evaluated. Numerical results show that manufacturing errors and misalignment have a remarkable effect on the transient behavior of dynamically loaded journal bearings, and the coupling effect will be more consistent with practical engineering. It can be found that the distribution form of the micro-groove surface directly affects the friction reduction effect of bearing systems. The numerical model can serve as a meaningful guideline for the optimum design of dynamically loaded journal bearing with micro-groove.