Epoxy asphalt (EA), which is usually prepared by diglycidyl ether of bisphenol A (DGEBA), curing agent and asphalt, is a kind of high-performance pavement material in highway construction. However, because of rigid molecular structure of DGEBA, poor compatibility with asphalt and high cross-linking density of three-dimensional network, cured EA usually has high strength but poor toughness especially at low temperature. In order to solve the problem of insufficient toughness of EA below glass-transition temperature (Tg) and eliminate the potential brittle fracture of EA mixture, linear aliphatic epoxy compounds, which have low viscosity, good molecular flexibility, similar solubility parameter and polarity with asphalt or DGEBA resin, can be used as phase structure controller and toughner to modify EA. By introducing a little of linear aliphatic epoxy compound, such as 1, 4-butanediol diglycidyl ether (BDDGE) or 1, 6-hexanediol diglycidyl ether (HDDGE), not only the viscosity of EA could be significantly decreased during the curing process, but also the phase compatibility of EA could be improved. An obvious reduction in storage modulus (E′) at low temperature and decreased Tg also prove that BDDGE or HDDGE modified EA have better toughness than neat EA at low temperature. The optimum amount of linear aliphatic epoxy compound based on its mixture with DGEBA should be 10–15 wt%.