Abstract: It is difficult to describe the microstructure characteristics of soil aggregates using traditional methods. Although classification and analysis of <0.25 mm aggregates are necessary, knowledge about them is insufficient. Thus, accurate evaluation of the effect of agronomic measures on soil aggregate structure characteristics using modern microscopic techniques is important for soil management via the adoption of scientific methods. A long-term positioning field experiment in 2016 in the Shiyang River Basin of desert oasis area of the Hexi Corridor was conducted to investigate the effect of green manure retention practices on soil aggregate characteristics under a wheat-green manure-maize rotation system. The different practices included tillage with full quantity of green manure incorporated into the soil (TG), no-tillage with full quantity of green manure mulched on the soil surface (NTG), tillage with above-ground green manure moved and roots incorporated into the soil (T), no-tillage with above-ground green manure moved (NT), and conventional tillage without green manure (CT, the control). In 2019 to 2020, a scanning electron microscopy was used to analyze the microcosmic images of 0–30 cm soil during maize tasseling and silking stages to qualitatively reveal the apparent characteristics. Nano Measurer software was used to quantitatively analyze the soil particle size and aggregate characteristics. Results showed that most of the soil particle size under CT was less than 0.25 mm, of which 23.9%−27.4% were sand, a kind of smooth surface and regular shape with particle size ranged from 0.05 to 0.25 mm. Others were silt and clay (USDA), and the number of soil aggregates accounted for 9.1%−9.6% of the total particles. Compared to those under CT, the soil particles of NT and T were very fine sand with particle size ranging from 0.05 to 0.1 mm, and the number of soil aggregates under the two treatments was improved by 10.1%−23.3% and 14.4%−17.3%, respectively. The TG and NTG treatments facilitated the reduction in the particle size of single-grain sand in the maize field. These small single grains constituted large aggregates with rough, porous, and uneven surfaces and were attached by a lot of silt and clay. The particle size of large aggregates ranged from 0.1 to 0.25 mm. Compared to that under CT, the number of soil aggregates under TG and NTG treatments was improved by 25.8%−50.9% and 34.1%−43.4%, respectively. In addition, soil under NTG exhibited structural performance and potential to form large aggregates with particle size >0.25 mm. Therefore, in a desert oasis area, a full quantity of green manure was incorporated into the soil or mulched on the soil surface with no tillage after wheat-green manure cropping system, and the soil under both the systems had superior structural characteristics of soil aggregates compared to that under the control system.