Afforestation improves the soil organic carbon (SOC) sequestration by affecting aggregates formation. However, the impact of the establishment and development of windproof sand fixation forests on soil carbon (C) flow and sequestration in desert regions are largely unclear. The space-for-time method was used to elucidate changes in bulk soil, aggregate-associated organic carbon (OC) content, stock, and C flow with afforestation years and the main influencing factors. We sampled from 0–20 cm, 20–60 cm and 60–100 cm in natural desert (CK) and windproof sand fixation forests after 3, 7, and 10 years of afforestation. The direction of C flow within the aggregates was quantified using the δ13C natural abundance method. Results showed that compared to the CK, afforestation increased in the bulk soil OC stock in the 0 − 100 cm by 2.97, 5.34, and 1.67 Mg·ha−1 at 3, 7, and 10 years of afforestation, respectively. The bulk soil OC content decreased gradually, but the stock increased with soil depth. Furthermore, C sequestration in this region mainly relied on the microaggregates OC. Microaggregates acted as both a “source” and a “sink” in desert ecosystems. During the 7 years of afforestation, the δ13C in the aggregates decreased with increasing soil depth, indicating older C in the subsoil. The variations in bulk soil OC stock were mainly regulated by ammonium nitrogen, nitrate nitrogen, and total nitrogen. Therefore, the results suggest that 7 years of afforestation may be the optimal choice among the three afforestation years compared for C sequestration.