Objective To address the problem of late strut thrombosis generated after the implantation of biodegradable vascular stents, a stochastic finite element model was established to perform biomechanical analysis from the perspectives of molecular weight and stress. Methods A mathematical model of the degradation process of biodegradable vascular scaffolds using poly lactic acid (PLA) was established and the mathematical model was imported, and a finite element model was constructed using COMSOL software. The model was stochastically used to analyze the effects on molecular weight and stress distribution in the degradation process under different stochastic parameters and standard deviations. Results During the degradation process of degradable polymer vascular scaffolds in human body, the random variables Mn0 and 8% standard deviation had the most significant effects on the distribution of molecular weights; randomization of the parameters led to a wider distribution range of the fracture strength during the degradation process of polymer vascular scaffolds, and the minimum value of fracture strength was lower. Conclusions The inhomogeneity of molecular weight distribution in polymer vascular stent materials leads to differences in mechanical properties at different locations of the stent, which in turn causes stress concentration within the material, ultimately leading to non-uniform fragmentation of the stent during degradation, which becomes a determining factor for stent thrombosis in later stages. This study provides theoretical guidance for designing next-generation biodegradable vascular stents.