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Subsurface flow problems usually involve some degree of uncertainty. Consequently, uncertainty quantification is commonly necessary for subsurface flow prediction. In this work, we propose a methodology for efficient uncertainty quantification for dynamic subsurface flow with a surrogate constructed by the Theory-guided Neural Network (TgNN). The TgNN here is specially designed for problems with stochastic parameters. In the TgNN, stochastic parameters, time and location comprise the input of the neural network, while the quantity of interest is the output. The neural network is trained with available simulation data, while being simultaneously guided by theory (e.g., the governing equation, boundary conditions, initial conditions, etc.) of the underlying problem. The trained neural network can predict solutions of subsurface flow problems with new stochastic parameters. With the TgNN surrogate, the Monte Carlo (MC) method can be efficiently implemented for uncertainty quantification. The proposed methodology is evaluated with two-dimensional dynamic saturated flow problems in porous medium. Numerical results show that the TgNN based surrogate can significantly improve the efficiency of uncertainty quantification tasks compared with simulation based implementation. Further investigations regarding stochastic fields with smaller correlation length, larger variance, changing boundary values and out-of-distribution variances are performed, and satisfactory results are obtained.