The hardness, toughness, wear resistance, and fatigue behavior of materials can be improved through a deep cryogenic treatment (DCT). During this treatment, low temperatures (−100 °C to −196 °C) are maintained and then increased to room or higher. In this work, an indirect-extrusion plate of 7A99 ultra-high strength aluminum alloy was subjected to a T6 (peak aging) treatment and a T6-DCT treatment. The influence of the T6-DCT treatment on the mechanical properties, grain morphologies, precipitates, and atom–cluster distribution was investigated via tensile testing, electron backscatter diffraction, transmission electron microscopy, and three-dimensional atom probe analysis. The tensile strength (maximum: 705 deep cryogenic treatment), yield strength (maximum: 678 MPa), and elongation (maximum: 14%) of the T6-DCT-treated alloy were higher than those of the T6-treated alloy. Moreover, the T6-DCT treatment resulted in (i) grain size refinement and increased uniformity of the microstructure (homogeneous distribution of η’-MgZn2- and η-phase precipitates), and (ii) reduced segregation degree of Zn, Mg, and Cu atoms in the matrix (fraction of small atom clusters (sizes: 10–20 nm, 20–50 nm) increased, fraction of large clusters (size: >1,000 nm) decreased). Therefore, DCT can refine the precipitates and increase the uniformity of the precipitate distribution, thereby improving the strength and plasticity of the alloy.