Abstract To improve the strength and toughness of epoxy resins and their composites, a series of silane‐modified polyurethanes (SM‐PUs) was synthesized. The SM‐PUs were then incorporated into the epoxy resin system to prepare silane‐modified polyurethane toughened epoxy resins and their composites. The relationship between the structures of the SM‐PUs and the properties of the resin systems and their composites was investigated. The results revealed that the addition of the SM‐PUs can effectively improve both the strength and toughness, as well as the corrosion resistance of resin systems. Among all resin systems, PUSiM/EP/DDM with two benzene rings and PUSiT/EP/DDM with a benzene ring exhibited the highest strength and toughness, respectively. The maximum values of the tensile strength, elongation at break, critical stress intensity factor (K IC ), critical energy release rate (G IC ), and impact strength of the resin systems reached 82.08 MPa, 10.06%, 1.64 MPa·m 1/2 , 1.77 kJ·m −2 , and 26.87 kJ·m −2 , respectively, showing an improvement of 23.5%, 89.5%, 53.3%, 284.8%, and 36.4% over those for EP/DDM. Moreover, PUSiT/EP/CF/DDM prepared by using PUSiT/EP/DDM with the best toughness showed the highest mechanical performance. Simultaneously, the strengthening and toughening mechanisms were explored through SEM and the simulated internal network. Highlights A series of silane‐modified polyurethanes was synthesized for toughening EP. Addition of SM‐PUs enhanced the mechanical properties of resins and composites. The composite with high‐toughness resin showed the best strength properties. SEM and the simulated internal network revealed toughening mechanisms.