The laser-induced damage threshold (LIDT) of coating for high-power laser system depends greatly on the surface quality of substrate. In this work, pits were precisely fabricated on fused silica substrate using a femtosecond laser processing bench. The LIDT of e-beam deposited high-reflective (HR) multilayer coating on substrate with pits was examined with respect to the electric-field distribution and mechanical property. Layer deformation was observed in coatings on substrate with pits. Simulation results demonstrated that the decrease in LIDT of the coating on substrate with pits can be attributed to E-field distribution enhancement and local mechanical property degradation induced by the layer deformation. A “suture” layer is proposed to solve the layer deformation induced problem, decreasing the E-filed distribution and improving the mechanical property. Surface morphology, global coating stress and high-resolution cross sections were characterized to determine the effects of substrate pit suturing. Investigation results demonstrated that the deformational level in coating on pitted substrate is greatly reduced by introducing the “suture” layer, and therefore the LIDT of HR coatings on substrate with pits is enhanced.