Purpose <p>Extensive manure application in greenhouses increases soil binding agents (e.g. soil organic carbon, SOC; glomalin-related soil protein, GRSP) but also raises dispersing agents (e.g. exchangeable Na⁺), potentially affecting soil structure stability. While individual effects have been studied, the combined impact of soil binding and dispersing agents on soil aggregate stability under greenhouse conditions remains unclear.</p> Methods <p>This study was conducted in two greenhouse areas (2–50 years of use) in northern China, covering loam and sandy loam. We assessed the effects of long-term manure application on binding agents, dispersing agents and soil aggregate mean weight diameter (MWD) and analyzed their combined impact on MWD.</p> Results <p>Soil binding agents in the greenhouse under long-term manure application initially increased and then stabilized, while dispersing agents continued to increase. In the loam soil, SOC and GRSP contents increased steadily over 20 years, then stabilized, stabilizing aggregate MWD at 50–67% higher than open-field. However, in the sandy loam, SOC and GRSP contents remained stable over 2–32 years, but a decline in MWD after 30–32 years, highlighting the vulnerability of coarse-textured soils to dispersive forces. SOC, GRSP, and exchangeable Na⁺ were key factors for MWD; in loam, SOC/Exchangeable Na⁺ &gt;14.67 and GRSP/Exchangeable Na⁺ &gt;3.77 maintained stability, while SOC/Exchangeable Na⁺ &lt;5.87 and GRSP/Exchangeable Na⁺ &lt;2.03 in sandy loam caused decline. Greater MWD response to GRSP/Exchangeable Na⁺ ratio indicates GRSP contributed more than SOC.</p> Conclusion <p>Greenhouse soil requires attention to the ratio of organic matter to exchangeable Na⁺, as exceeding a certain threshold can damage soil structure.</p>