The work aims to control the cross-linking network structure of silicone resin by toughening and modifying the phenyl silicone resin-based microwave absorbing coating with heat-resistant small molecules that can react with organic silicone monomer, and compound the modified silicone resin with heat-resistant absorbent to develop heat-resistant microwave absorbing coatings with high flexibility, high adhesion and thermal stability. Toughening modifiers with different end groups or chain length were grafted to silicone resin by hydrosilylation addition reaction to change the crosslinking networks of the matrix. The properties of the coatings were tested by infrared spectrum, SEM, mechanical properties and dynamic mechanical thermal analyzer. With the increase in content of vinyl-terminated poly (dimethyl siloxanes), the flexibility of the coating was improved, whereas the heat-resistant and adhesion were reduced. When the content of vinyl-terminated poly (dimethyl siloxanes) increased to 45 wt. %, the flexibility of the 1 mm coating reached 20 mm, with adhesion as high as 7.73 MPa and impact resistance of higher than 50 kg∙cm. After working at 300 °C for 15 h, the flexibility of the coating increased from 1.08 mm for unmodified coating to 1.35 mm. Moreover, the modified coatings maintained good flexibility after heat treatment. Modifying the crosslinking networks of silicone resin with heat-resistant small molecules can effectively control the mechanical properties of heat-resistant microwave absorbing coatings and provide references for toughening and engineering applications of heat-resistant microwave absorbing coatings.