Statistical size and geometrical size are the main factors affecting the service life of mechanical structure calculation. To explore the reliability of the lifespan of beam structures, a probability lifespan numerical calculation method based on Vector Form Intrinsic Finite Element Method (VFIFEM) was proposed, and the method was verified through full lifespan experiments on I-beam welded structures. First, a fatigue fracture model that considers the coupling of residual stress (RS) and cyclic load variations was established. Based on this fatigue fracture model, a probability lifespan calculation model for beam elements was defined by proposing a cross-sectional shape correction coefficient and a position correction coefficient. The proposed probability lifespan model for beam elements was used to calculate the I-beam welded structure, and the calculated results were compared with the full lifespan experiment results, which were close in statistical results, with all experimental results falling within the [10%, 90%] interval except for one experiment. This method effectively couples the influence of statistical size and geometric size on probability lifespan, providing a new approach for the structure probability lifespan calculation in the future.