Evolution of microstructure, elemental and phase composition of dense zirconia-based composite under irradiation with electron beam were investigated. Tetragonal zirconia-based composite reinforced by 5 wt% alumina nanofibers and 0.5 wt% single-walled carbon nanotubes was prepared by spark plasma sintering at a temperature of 1500°C. Irradiation of the composite was carried out with a low-energy pulsed electron beam of submillisecond duration in the following mode: beam energy density 15 J·cm−2; pulse duration 200 μs; pulse repetition rate 0.3 s−1; pulses quantity 10, 20, 30 and 40; residual gas pressure (argon) in the working camera 10−2 Pa. It has been established that electron beam treatment leads to the formation of modified multilayered surface, the thickness of which varies from 6 to 40 μm. Redistribution of Al atoms in the modified surface layer was detected. The phase evolution dependent on the quantity of irradiation pulses and manifested in the crystalline structure of material.