The lubrication is essentially important to enhance the anti-tribology abilities of the journal bearing by forming a thin film to separate the contact surface. However, the journal bearing usually works under severe operating conditions, and the journal misalignment may happen due to various reasons, such as the induced errors during the manufacturing/installation process and uneven deformation caused by the non-uniform distributed load, especially for those journal bearings used in heavy-duty machinery. Whenever the thin lubrication film cannot afford to carry out the loading, solid-solid contact occurs, which is usually referred to as mixed lubrication. In this paper, a multi-pads journal bearing used in the planetary gearbox of the circulating water pump at nuclear power plant was focused on and the safe application of nuclear energy requiring the bearing to have a reliable ability to maintain the rotating motion of gear sets, and the lubrication in such a bearing system deserved special attention. A numerical mixed lubrication model with misaligned journal involved was thus established by connecting the elastohydrodynamic lubrication and the asperity contact. The equation of film thickness for each pad was properly formulated and the influence coefficient method was also employed to estimate the elastic deformation of each pad surface, which was then introduced to update the film thickness equation. The average Reynolds equation that governed the lubrication pressure was discretized by the finite difference method and solved based on the pre-specified boundary conditions. Later, the solid direct contact pressure was obtained through the asperity contact model. The developed numerical model was well validated by comparing the simulation results with those reported in references. Then, the lubrication performance of multi-pad journal bearing with variable clearance under different operation conditions was investigated, and the effects of various factors, including journal bearing clearance, misaligned journal angle and rotating speed, had been revealed in detail. It was found that most of the loading was supported by several specific bearing pads under the journal, and the influences brought by those factors on the loading-sharing ratio appeared to be different. The loading-sharing ratio of the prime loading pad would decrease when reducing the bearing clearance and increasing the rotation speed. However, it would almost remain the same loading-sharing level when the misaligned angle changed. The results also demonstrated that the misaligned journal angle dominated the influences on the lubrication performance of multi-pad journal bearing, leading to an asymmetric distribution of the film thickness and fluid pressure, and an obvious end-side effect at one side edge of journal bearing was observed, which probably leaded to a large increase on the level of maximum fluid pressure. The solid contacting was more likely to appear at the boundaries where the fluid pressure was at a higher level, resulting in severe wear damage there. The evolution of the coefficient of friction with the rotating speed increasing was investigated and the results implied that there was an optimal rotating speed for journal bearing system. The lubrication performance could be improved by appropriately adjusting the clearance of each bearing pad, which leaded to lower maximum fluid pressure and larger loading capacity. The conclusions in current study also potentially provided guidance for the lower friction design of journal bearing.