The invention relates to a distributed multi-branch VPN communication method and system, and a storage medium, and the method comprises the following steps: detecting the communication quality of each transit server, and calculating the link communication quality between different transit servers; responding to communication joining of the first terminal and the second terminal, searching a plurality of paths with the best communication quality between the first terminal and the second terminal according to the link communication quality between the different transit servers, and establishing a plurality of branches; and realizing the transmission mode of the plurality of branches as a VPN layer, and transmitting a link layer data packet on the VPN layer to realize communication between the first terminal and the second terminal. The multi-branch communication and the VPN layer are combined to ensure that a point-to-point communication link is not influenced by a single-point fault, ensure that the network redundancy bandwidth is fully utilized, and ensure that when a certain communication link section fails, redundancy switching can be performed without communication link breakage at all.