The thiol-epoxy click chemistry is promising for microelectronic packaging due to its outstanding properties, while there is little knowledge on silicone/epoxy composite fabricated via this approach. Herein, a thiol-functionalized silicone resin (MDT-SH) is synthesized and compounded with epoxy resin to form silicone/epoxy composite. The thermal-curing behaviors, mechanical properties and LED encapsulation of the developed composite are studied detailedly. The thermal-curing kinetics indicate that the thiol-epoxy polymerization in silicone/epoxy composite tends more to the first-order reaction and its active energy is about 60.3 kJ/mol. The mechanical properties of the composite are varied with the molecular structure of MDT-SH and thiol/epoxy ratio. Moreover, the composite has excellent transparency in visible region, and its transparency is little affected by thermal and UV ageing. More importantly, the transparency is only slightly decreased after the composite is serviced at normal temperature and pressure for 2 years. The light output power of LEDs encapsulated by this composite is comparable to the commercial counterparts like Dow Corning OE-6550, but its thermal-curing time and temperature are much lower than the latter, contributing to cost reduction. Therefore, this silicone/epoxy composite based on thiol–epoxy click chemistry would greatly improve the microelectronic packaging.