The mechanical stability aggregates (MSAs) represent a critical factor in maintaining soil structure stability. A seven-year field trial was conducted (2017-2023) to investigate the impact of MSAs on maize (Zea mays L.) yield across three distinct soil layers, utilising manure as a substitute for chemical fertilisers. Five treatments were established, each with a total nitrogen level of 225.00 kg ha(-1). They were as follows: no fertiliser (CK), 25/50/75/100 % manure nitrogen+75/50/25/0 % chemical fertiliser nitrogen (M25, M50, M75 and M100, respectively). The findings demonstrated that in 2017, the 2-5 mm MSAs under M50 exhibited an increase of 22.2 % (p <= 0.01) compared to the CK in the 0-10 cm pedosphere. In 2018, there was a significant increase of 27.5 % (p <= 0.01) in 0.5-1 mm MSA under M50 compared to M100 in the 20-30 cm pedosphere. All three pedosphere zones under manure substitution treatments had higher mass median diameters (MMD) and geometric mean diameters (GMD) than CK. The most pronounced indices for soil aggregate stability and a significant improvement in soil quality were observed in 2020. Moreover, except for the 1-2 mm MSAs in the 20-30 mm pedosphere, constituents of MSA exceeding 1 mm in all three pedospheres exhibited a positive correlation with yield (p <= 0.01). A significant negative correlation was observed between >5 mm MSA and CO2 and CH4 emission flux in the 10-20 cm soil layer. It can be assumed that using manure to replace synthetic fertilisers can be a practical guideline for optimising farm management practices in semi-arid regions.