The long-term changes of nutrition exports from 1978 to 2009 were studied by monitoring and SWAT model inversion in the Lianshui River basin (579 km2) in the red soil hilly region with middle subtropical climate. The relative influences of different climate and human factors on the nutrition exports were quantified by aggregated boosted trees (ABT) and partial canonical correspondence analysis (PCCA). The monitoring results showed that the amounts of annual average total nitrogen and phosphorus loss were 1.10 t/(km2·a) and 0.12 t/(km2·a) during 2003 to 2009. The SWAT model inversion showed a marked reduction of nutrient export with the long-term practices (forest restoration) of water and soil conservation in the basin since 1983. The mean annual total nitrogen and phosphorus export were reduced by 43.8% and 51.0% respectively during the first remediation period (1983—1990) in comparison with the pre-remediation period (1978—1982), and were reduced by 28.3% and 27.2% respectively in the second remediation period (1993—2002) in comparison with the first one. As a whole, the human factors showed higher influence on the basin nutrition export than the climate factors. Human factors explained 48.7% and 38.9% of the variation of total nitrogen and phosphorus exports, respectively, whereas climate factors explained 23.2% and 22.8% respectively. The ABT analysis showed that the main important factors include population, fertilization, sparse woodland area, land use index and vegetation index. Therefore, it is important to reduce nutrition export by changing the structure of land use, besides controlling the population density and scientific and reasonable fertilization.