Silicone rubber (VMQ) possesses a saturated −Si− O− main chain and natural rubber (NR) contains a large amount of CC bonds; thus, due to the large difference in saturating degree and main chain characteristics, it is difficult to compound them and obtain homogeneous composites. In this study, a trimercapto modifier [trimethylolpropane tris(3-mercaptopropionate)] (TMPMP) was chosen to enhance the interfacial compatibility of NR/VMQ composites via a thiol-ene click reaction. Due to the reactivity discrepancy of TMPMP with NR and VMQ, a two-step strategy of compatibilization was adopted. After modification, VMQ exhibited a smaller domain size and a more even distribution in the NR matrix, and the corresponding static mechanical properties and dynamic fatigue crack propagation resistance of NR/VMQ composites were improved. Furthermore, it is pointed out that the crack growth rate (dc/dN) shows a positive relevance with the viscoelastic parameter loss compliance modulus (J"): a less J" value means that more energy dissipation occurred in the linear viscoelastic region in front of the crack tip, resulting in less dc/dN and a better crack propagation resistance.