Abstract: Agricultural structure is considered to play an important role in regulating the dual pressures of economic growth and non-point source pollution from agricultural development. The total amount of surplus nitrogen, which is the main source of agricultural non-point source pollution, was calculated according to Truog's nutrient balance theory. The impulse response function and variance decomposition methods, based on the vector error correction model (VECM), were used to investigate and explain the relationship among agricultural economic growth, agricultural non-point source pollution, and agricultural structure in Fujian Province from 1998 to 2017. The research results showed that: 1) there was a relationship of long-term equilibrium among agricultural economic growth, agricultural non-point source pollution, and agricultural structure. 2) The Granger causality test showed that: agricultural non-point source pollution and economic growth were Granger causes for each other; agricultural structure was the Granger cause of non-point source pollution and agricultural economic growth; and agricultural economic growth was the Granger cause of agricultural structure. 3) The results of variance decomposition showed that there was little impact of agricultural economic growth and agricultural structure on agricultural non-point source pollution. The variance contribution of the impact of agricultural economic growth and agricultural structure on agricultural economic growth was 4.31% and 4.02%, respectively. The agricultural non-point source pollution had a great effect on agricultural economic growth. In the next 10 years, the variance contribution from agricultural non-point source pollution would reach 47.02%. 4) In the light of these findings, potential policy suggestions include: continuing to rectify agricultural non-point source pollution; encouraging the development and application of green agricultural technology and methods; increasing the role of the construction of agricultural infrastructure and farmer organization, introducing more detailed and guided financial policies to support agriculture; and strengthening the awareness on green consumption.