Fatigue cracking is one of the most notable distresses in steel bridge deck pavement (SBDP), necessitating the development of high performance pavement materials to extend service life. In this paper, the fatigue resistance characteristics of natural rock asphalt (NRA)/SBS systematically evaluated. Twelve types of composite-modified asphalt binders were prepared by incorporating Iranian rock asphalt (IRA), Buton rock asphalt (BRA), and SBS as modifiers. IRA and BRA were added at 5 wt%, 10 wt%, and 15 wt%, while SBS was introduced at 2 wt% and 3 wt%. The modified asphalt binders subjected to time sweep (TS) test and linear amplitude sweep (LAS) test to comparatively analyze fatigue damage and fatigue life. DSR-C model was applied to calculate the fatigue crack length. The research also comparative evaluate differences and correlations between fatigue crack length indexes and conventional fatigue life indexes. The results showed that NRA enhanced the fatigue performance of modified asphalt binders. With the increase of NRA content, the fatigue properties of modified asphalt also become better. S₃I₁₅ is better than other composite modified asphalt binders in both fatigue life and fatigue cracking indexes, demonstrating that it offers the best resistance to fatigue damage. The fatigue cracking index calculated by the DSR-based cracking (DSR-C) model could effectively evaluate the fatigue performance of NRA/SBS composite modified asphalt binders. NRA/SBS composite modified asphalt could be widely used in steel bridge deck pavement.