Glomalin-related soil protein (GRSP) is a hydrophobic protein released by arbuscular mycorrhizal fungi. It is an important component of the soil carbon pool, and it improves the soil aggregate structure; however, it remains unclear whether GRSP can enhance soil carbon sequestration and improve soil quality during rapid urbanization. The built-up area in Nanchang, China was the study area, and the proportion of impervious surface area was the parameter of urbanization intensity. A total of 184 plots (400 m2) were set up to collect soil samples (0–20 cm) for analysis. Aggregates of five particle sizes were sieved, and the percentage amounts of soil organic carbon (SOC) and GRSP for them were determined. The results showed that the easily extractable GRSP (EE-GRSP) and total GRSP (T-GRSP) contents of the four aggregates of <2 mm were 22–46% higher in low urbanization areas than those in high urbanization areas (p< 0.05), indicating that the higher urbanization intensity was associated with the lower GRSP content of different aggregates. The GRSP was significantly positively correlated with SOC (p< 0.05). Moreover, the contribution of GRSP to the SOC pool in the <0.25 mm aggregate was significantly higher than that in other aggregates. In addition, the EE-GRSP content was significantly positively correlated with mean weight diameter (MWD) and geometric mean diameter (GMD) in the four aggregates of <2 mm, whereas it was negatively correlated with fractal dimension (D) in the >2 mm, 1–2 mm and <0.053 mm aggregates. The T-GRSP content showed significant correlations only with MWD, GMD, and D in the 1–2 mm aggregate. This study revealed that increasing urbanization intensity can significantly reduce the GRSP content of different sized aggregates. Moreover, the GRSP content significantly promoted SOC sequestration, and the EE-GRSP content more significantly promoted soil aggregate stability than that of the T-GRSP. These findings provide new ideas for exploring the improvement of soil quality during the process of urbanization.