Groundwater contaminant source identification (GCSI) has practical significance for groundwater remediation and liability. However, when applying the simulation-optimization method to precisely solve GCSI, the optimization model inevitably encounters the problems of high-dimensional unknown variables to identify, which might increase the nonlinearity. In particular, to solve such optimization models, the well-known heuristic optimization algorithms might fall into a local optimum, resulting in low accuracy of inverse results. For this reason, this paper proposes a novel optimization algorithm, namely, the flying foxes optimization (FFO) to solve the optimization model. We perform simultaneous identification of the release history of groundwater pollution sources and hydraulic conductivity and compare the results with those of the traditional genetic algorithm. In addition, to alleviate the massive computational load caused by the frequent invocation of the simulation model when solving the optimization model, we utilized the multilayer perception (MLP) to establish a surrogate model of the simulation model and compared it with the method of backpropagation algorithm (BP). The results show that the average relative error of the results of FFO is 2.12%, significantly outperforming the genetic algorithm (GA); the surrogate model of MLP can replace the simulation model for calculation with fitting accuracy of more than 0.999, which is better than the commonly used surrogate model of BP.