Al-12Zn-2.4Mg-1.1Cu alloy was prepared by the spray deposition method. The microstructure and mechanical properties of the spray-deposited alloy after two-step aging treatment were investigated by high-resolution electron microscopy and hardness tests. The results show that the η′ phase and GPⅡ zones are major precipitates in the alloy after the ageing treatment at 120 oC(14 h). The hardness of the alloy increases to the top and the grain boundary precipitate phases are of continuous distribution. After the two-ageing treatment at 120 oC(14 h)+160 oC(0.5 h), 120 oC(14 h)+160 oC(16 h) and 120 oC(14 h)+160 oC(24 h), the hardness of the alloy is reduced by 5.92%, 11.13% and 15%, respectively compared with those under peak-aged condition and the major precipitates are the fine η′ phase, the coarse η′ phase and the coarse η phase, respectively. The distributions of grain boundary precipitate phases are discontinuous. The grain boundary precipitate phases and the precipitate phases of grain interior have grown up obviously. After the two-ageing treatment at 120 oC (14 h)+160 oC (16 h) and 120 oC (14 h)+160 oC (24 h), the precipitation free zones are also observed. Based on the measurement of TEM images, the lattice parameter of η phase are 0.520 and 0.860 nm and those of η′ phase are 0.490 and 1.402 nm. After the deconvolution processing on η and η′ phase, the image resolution can be improved. Then, the η and η′ phase were simulated by jems, and the basic position of atoms can be determined.