A new type highly crosslinked and uniform thermoset epoxy microspheres (EMs) was prepared through the thermal curing between a trifunctional epoxy resin (TGPAP) and an aromatic amine hardener (DETDA), by precipitation polymerization in a low molecular weight polypropylene glycol (PPG-600) medium. The formation of EMs and the phase separation process were investigated in detail. The structure and thermal properties of EMs were characterized, and the result showed that EMs was active microspheres with hydroxyl and amino groups on its surface, and it had a high glass transition temperature Tg of 205 °C and high thermal stability. EMs was further used to toughen brittle epoxy resins. The effect of EMs on the curing behavior, mechanical and thermal properties of epoxy resins was studied. EMs accelerated the curing and the effect reached maximum till 5 wt% amount. Mechanical and thermal performance measurements exhibited that EMs not only significantly improved the toughness of epoxy matrix, but also increased the Tg. When 5 wt% EMs was introduced, the impact strength rose from 17.8 kJ m−2 to 42.4 kJ m−2 and Tg increased more than 10 °C. The excellent toughening performance of EMs was attributed to its high stiffness and active surface.