In this article, the flame retardant poly(aminopropyl/phenyl)silsesquioxane (PA) was incorporated into thiol-ene (TE), to obtain a flame-retardant thiol-ene (FRTE) composite. The cone calorimeter (CONE) measurement results showed that, compared with neat TE, the peak of heat release rate (PHRR) and total heat release (THR) of FRTE have decreased by almost 23.7% and 14.5%, respectively. Thermogravimetric analysis (TGA) results further confirmed that the flame retardant PA could induce the initial thermal degradation of TE, and increased the amounts of residual char. Moreover, the activation energies of FRTE were calculated through the Kissinger and Flynn–Wall–Ozawa methods. Compared with the neat TE, the activation energies of FRTE were raised by the addition of PA. It indicated that the flame retardant PA promoted cross-linking reactions of TE, to form a compact char layer and retarded further the thermal degradation of the polymer matrix.