The cladding acts as the first barrier to prevent the release of radioactive fission products, requiring its structural integrity to be maintained throughout the whole operation period of nuclear reactor. Therefore, cladding failure due to PCI (pellet claading mechanical interaction) should be avoided as much as possible in fuel design and operating conditions. At the same time, it is necessary to achieve effective control of the cladding stress by limiting the power growth rate etc. However, in the manufacturing process of fuel rod, the MPS (missing pellet surface) defect is inevitably generated. This defect may lead to a substantial increase in the local stress of the cladding, which in turn exceeds its corresponding stress limit, resulting in cladding failure. Accurate simulation of fuel performance caused by such defects will help prevent such failures. The traditional fuel performance analysis codes are based on a 1.5D analysis framework and cannot handle the local asymmetry problem of fuel such as the MPS defect. In order to accurately simulate the PCI phenomenon caused by the MPS defect, this research establishes a fuel performance analysis code based on the ABAQUS software and this code is suit for the 2D and 3D conditions. Based on the established analysis code, the irradiation-thermal-mechanical behavior of nuclear fuel under typical II transient conditions was studied, and the sensitivity analysis of the influence of different MPS sizes on the local stress of cladding was carried out. The simulation results show that :(1)the mises stress, contact pressure and equivalent creep strain of the cladding may be unevenly distributed due to the MPS defect.(2)the MPS defect will result in a more severe contact pressure on cladding during power transient period, which may lead to failure of cladding and should be prevented. The simulation method established in this research could be very help for the performance analysis for the nuclear fuel rods.