Natural gas, an efficient, eco-friendly and clean green energy, has become one of the important energy structures of various countries in the world, accurately predicting the production of natural gas can help the national energy agency solve “gas shortage” problem. To accurately predict natural gas production in China, this paper establishes an optimized grey system model with weighted fractional accumulation generation operation (abbreviated as WFNGBM(1,1,N)). The proposed model has all the advantages of the GMP(1,1,N) model, NGBM(1,1) model and weighted fractional accumulation generation operation, which makes it have excellent prediction performance. Moreover, five outstanding intelligent optimization algorithms (whale optimization algorithm, marine predators algorithm, grasshopper optimization algorithm, equilibrium optimization algorithm and arithmetic optimization algorithm) are used to solve the hyperparameters of the WFNGBM(1,1,N) model. It is found that the WFNGBM(1,1,N) model has the characteristics of convertibility and small sample modeling, which indicates that it is a small sample prediction model with strong compatibility. After confirming the feasibility of the proposed model compared with its competing models by using natural gas production in Germany, Italy and Canada as examples, the proposed model is used to study China’s natural gas production. The results show that this model is very suitable for predicting and analyzing natural gas production in China. Based on this, the WFNGBM(1,1,N) model is used to estimate China’s natural gas production in the next three years, and some reasonable suggestions are given according to the development trend of natural gas production.