Abstract The gap in the development level of digital economy aggravates the inter-regional transfer of value-added tax, which makes the imbalance of regional distribution of value-added tax more prominent. Based on the provincial panel data from 2010 to 2020, this paper uses the spatial durbin model and the mediation model to empirically test the promotion effect and spatial effect of the digital economy on the regional distribution of VAT, as well as the intermediary mechanism of the regional transfer of VAT. The results show that the improvement of the relative development level of digital economy will significantly increase the distribution share of value-added tax in this region, but it has obvious siphon effect on other areas. The intermediary test indicates that the regional transfer of VAT is an important intermediary mechanism that affects the regional distribution of VAT. Among the effects on the regional distribution share of VAT, 18.03% is achieved by influencing the transfer of VAT between regions. The above research conclusions provide a theoretical and empirical basis for deepening the VAT reform, improving the fairness of the VAT tax system, and establishing a good regional VAT distribution relationship.