Understanding the inequalities of carbon neutrality within cities is essential for implementing differentiated carbon reduction policies. Here we develop an integrated model to conduct a fine-resolution (250 m, monthly) assessment of net carbon emissions (NCE) for three major urban agglomerations in China. Our results precisely depict the seasonal patterns of NCE and highlight the diverse urban carbon dynamics that contribute to inequalities in carbon neutrality. Nearly half of the 48 cities exhibited NCE exceeding 1000 gC∙m⁻²∙a⁻¹, while only 5 cities functioned as carbon sinks. Theil index analysis reveals that intra-city inequalities are more pronounced in industrial cities with Theil index over 0.11, while inter-city disparities are primarily driven by economic and industrial imbalances, particularly in the Pearl River Delta, where Theil index has reached 0.18. This emphasizes the dominant role of high-emission cities in shaping regional inequalities. These findings provide actionable insights for urban afforestation and emission mitigation policies aimed at achieving carbon neutrality.