A regional dynamic perimeter control method and system for preventing boundary links queuing overflow. The method includes: estimating the number of queuing vehicles of boundary links using a Kalman filtering extension method using traffic flow information, and calculating a maximum of receivable vehicles; dividing the boundary links utilizing an estimated number of each boundary link's queuing vehicles and the maximum number of receivable vehicles obtaining a boundary link set with sufficient storage and a boundary link set with insufficient storage; obtaining a critical accumulation of a region according to a preset Macroscopic Fundamental Diagram (MFD) model of the region, and predicting the estimated region accumulation in a sampling period; and controlling a regional boundary intersection traffic flow operation using a deviation between the predicted and critical accumulation and boundary link sets. Deterioration of regional traffic flow is avoided, and the probability of overflow of boundary links is reduced.