The sacral alar-iliac screw (SAIS) fixation technique has evolved from spinopelvic fixation which originated from S2AIS to sacroiliac joint fixation, with more reports regarding its application of S2AIS than S1AIS. However, there is a lack of comparative evidence to determine which technique is superior for sacroiliac joint fixation. This study aimed to determine which of the screws was superior in terms of implantation safety and biomechanical stability for sacroiliac joint fixation. CT data of 80 normal pelvises were analyzed to measure the insertable range, trajectory lengths and widths of both S1AIS and S2AIS on 3D reconstruction models. Φ 6.5mm and 8.0mm screws were implanted on the left and right sides of fifty 3D printed pelvic models respectively to observe for breach of screw implantation. Ten synthetic pelvis models were used to simulate type C Tile injuries, and divided into 2 groups with an anterior plate and posterior fixation using one S1AIS or S2AIS on each side. The stiffness and maximum load of the plated and fixated models were measured under vertical loading. The trajectory lengths and widths of the S1AIS and S2AIS were similar (p > 0.05) and there was no breach for Φ 6.5mm SAIS. However, both the insertable range and trajectory length on the sacral side of S2AIS (234.56 ± 10.06mm2, 40.97 ± 2.81mm) were significantly less, and the breach rate of the posterior lateral cortex of the Φ 8.0mm S2AIS (46%) was significantly higher than the S1AIS (307.55 ± 10.42 mm2, 42.16 ± 3.06mm, and 2%, p < 0.05). The stiffness and maximum load of S2AIS were less than S1AIS but the difference was not statistically significant (p > 0.05). S1AIS and S2AIS have similar screw trajectories and stability. However, S1AIS has a larger insertable range, less breach of the posterior lateral sacral cortex and longer trajectory length on the sacral side than S2AIS, which indicates S1AIS has higher implantation safety and a trend of better mechanical performance over S2AIS for sacroiliac joint fixation. Furthermore, S2AIS with an excessively large diameter should be used with caution for sacroiliac joint fixation.