Gross Ecosystem Product (GEP) assessment is important to the quantified assessment of the ecological protection policies benefits and to promote ecological benefits into economic and social evaluation system. The Southern Jiangxi Province is a typical southern hilly area, and regarded as an importantly ecological barrier in the upper reaches of the Ganjiang River and Dongjiang River for its high forest cover rate. We built an evaluation index system and used geographic information technology to qualify the value of GEP via three remote sensing images (from 2000 to 2018). By noticing the changes of GEP, we could assess the effectiveness of ecological protection measures. The results showed that:(1) the GEP of Gannan region in 2018 was 1096.326 billion yuan, which was c.a. 3.9 times to GDP. Climate regulation, water conservation, flood regulation and storage were the core service functions of the ecosystem in Southern Jiangxi Province. The total value of these 3 services accounted for 75.62% of the GEP that year; The per capita GEP of key ecologically functional counties is higher than that of non-key ecological functional counties, while the GEP per unit area is lower than that of non-key ecological functional counties; (2) The Green Gold Indexes (GEP/GDP) in 2000, 2010, and 2018 were 5.20, 4.19, and 3.91, respectively, representing a downward trend elapsed by time; (3) From 2000 to 2018, the GEP in Southern Jiangxi Province increased by 21.75% at comparable value, of which the average annual growth rates from 2000 to 2010 and 2010 to 2018 were 1.46% and 0.78%, respectively. The effectiveness of ecological protection showed a growth trend, but the rate decreased. GEP accounting could exhibit the condition and changes of the ecological environment in a certain period, the comprehensive implementation effectiveness by ecological protection, and provide a scientific basis for subsequently ecological protection in Southern Jiangxi Province.