Three kinds of epoxy prepolymers with high refractive index, diglycidyl ether of thiodibenzenethiol (DGETDBT), diglycidyl ether of thiobis-phenol (DGETP), and diglycidyl ether of oxydiphenol, were synthesized via a two-step method, and the relationship between the chemical structure and refractive index of epoxy prepolymer was discussed. Their chemical structures were characterized using Fourier transform infrared (FTIR) spectrometer and proton nuclear magnetic resonance spectrometer. The curing behavior of all the epoxy prepolymers cured with methylhexahydrophthalic anhydride (MHHPA) was studied using differential scanning calorimetry and was compared with that of diglycidyl ether of bisphenol A (DGEBA). Thermal and optical properties of these cured epoxy resins were investigated using thermogravimetric analyses, ultaviolet–visible scanning spectrophotometer, and Abbe refractometer, respectively. The results showed that three kinds of epoxy prepolymers had the similar thermal property and curing behavior. The sulfur atoms in DGETDBT and DGETP had contributed to an obvious increase in their refractive indexes, while the methyl group in DGEBA cut down its refractive index. The DGETDBT has the biggest refractive index (1.665), followed by the DGETP with 1.612. But the high cost and the lower thermal decomposition temperature of cured DGETDBT/MHHPA resin will limit its application. The refractive index of cured DGETP/MHHPA resin, with preferable thermal stability and acceptable price, is 1.595, which is higher than that of DGEBA/MHHPA resin (1.568). Therefore, DGETP resin can be expected to be a kind of the more effective encapsulant to light-emitting diode.