Glomalin-related soil protein (GRSP) is a widely distributed glycoprotein produced by arbuscular mycorrhizal fungi (AMF), plays a crucial role in soil structure, aggregate stability, and ecological restoration. However, few studies have explored soil nutrient and GRSP changes, as well as aggregate stability mechanisms during vegetation restoration in boreal forests. We used a "space-for-time substitution" approach and selected four habitats (grassland, Betula platyphylla forest, Larix gmelinii and Betula platyphylla mixed forest, and Larix gmelinii forest) in Greater Khingan Mountains of northeastern China to study the changes in AMF abundance, soil aggregate stability, EE-GRSP, and T-GRSP with succession. (1) The abundance of AMF, soil organic carbon (SOC), GRSP were increased with the successional process, and the stability of aggregates and soil structure (mean weight diameter, MWD, and geometric mean diameter, GMD) were also significantly enhanced. (2) During the successional process, there was an increase in the percentage of large aggregates (>0.25 mm) and a decrease in the percentage of microaggregates (<0.25 mm). Soil macroaggregates (>2 mm) were the primary contributors to SOC. (3) Compared with the stage of Betula platyphylla forest, SOC in the stage of Larix gmelinii forest was more protected by soil aggregates; the increase of GRSP caused by the water stress may be the main reason for the increase of soil aggregate stability. The successional process of boreal forests contributes to the stability of aggregates and the accumulation of carbon storage. We emphasize the importance of GRSP in the stability of soil structure and aggregates. Our research is significant for understanding the stability of aggregates and the ecological restoration mechanisms in boreal forests.