A network connection control system and method is provided. The network connection control system includes user equipments, base stations, a server and a processing unit. Each base station has a connection range and is configured to connect the user equipment located within the connection range. Each user equipment transmits a network parameter between it and every base station through the base station connected therewith to the server. The server generates a QUBO matrix according to all the network parameters and outputs the QUBO matrix to the processing unit. The processing unit processes the QUBO matrix based on a quantum annealing algorithm to obtain an optimized connection configuration of the user equipments and base stations. The server receives the optimized connection configuration and controls the connection range of each base station accordingly for making an actual connection configuration of the user equipments and base stations identical with the optimized connection configuration.