A fatigue test on the failure mode of flange shafts was conducted. The propagation characteristics of the initial crack at the junction between the shaft and the flange as well as its angle effect were studied. This study developed an analysis program of fatigue crack propagation, based on the APDL (ANSYS Parametric Design Language). It obtained the effective angle interval within which the initial crack is able to propagate. The fitting calculation formula was derived and the results showed that: (1) The initial crack at the junction between the shaft and the flange would propagate in the radial and axial directions; the unstable crack propagation would cause an abrupt fracture of the cross-section, failing connection; and the angle of initial crack was uncertain. (2) The crack followed the I-II-III mixed mode, which was dominated by mode I. An initial crack with a larger angle showed more noticeable II-III characteristics; KII and KIII affected the crack’s propagation angle in the radial and axial directions and they also affected the structure’s surface direction. (3) The deepest point A of the crack was located at the junction between the shaft and the flange. Its crack propagation can be divided into three stages: rapid growth (stage 1), steady decline (stage 2, buffer stage), and instability (stage 3). The initial crack angle not only affected the propagation rate at stage 1 but also influenced the fatigue life distribution of the structure during propagation. The larger the initial crack angle was, the smaller the proportion of buffer stage in the total fatigue life would be. Moreover, the propagation of crack with a larger initial angle reached instability faster after stage 1, which would cause an abrupt fracture of the cross-section. This was unfavorable for deciding the crack detection time or carrying out maintenance and reinforcement. (4) The crack propagation at the junction between the shaft and the flange was determined by the size relation between ΔKI and ΔKth, instead of the effective stress intensity factor. The effective stress intensity factor can partly reflect the law of crack propagation, but cannot serve as the only criterion for crack propagation; it must be combined with the effective angle interval, which was negatively correlated with the crack’s shape ratio, to determine whether the crack would propagate.