Large-scale human activities especially the destruction of forest land, grassland, and unused land result in a large amount of carbon release into the atmosphere and cause drastic changes in land use/cover in the Sanjiang Plain. As a climate change-sensitive and ecologically vulnerable area, the Sanjiang Plain ecosystem’s carbon cycle is affected by significant climate change. Therefore, studying the impact of the changes in land use/cover and climate on the carbon storage of the vegetation in the Sanjiang Plain is important. The dynamic impact of the changes in land use/cover and climate on the vegetation carbon storage was analyzed using Remote Sensing (RS), Geographic Information System (GIS) technology, and mathematical statistics and taking TM and MODIS Normal Difference Vegetation Index (NDVI) remote sensing data, temperature, and precipitation as main data sources. Research results showed the following observations. From 2001 to 2015, the vegetation carbon storage in the Sanjiang Plain continued to increase (total increase = 97.65 Tg). The carbon storage of the forest land increased by 98.73 Tg, and the carbon storage of cultivated land increased by 0.56 Tg. The carbon storage values of grassland and unused land decreased to 0.86 and 0.78 Tg, respectively. The increase in the carbon storage of cultivated land was caused by the increased area, and that of forest land was attributed to the increased carbon density. The decrease in the carbon storage of grassland and unused land was out of the decrease in its area. Therefore, the transform in land use types and vegetation carbon density changed the vegetation carbon storage. Through the pixel-by-pixel analysis of the invariant region, the carbon storage of various vegetations in the Sanjiang Plain was negatively correlated with the average temperature and positively correlated with the average precipitation. The partial correlation analysis of the changes in climate and land use/cover concluded that the changes in land use/cover and vegetation carbon density in the Sanjiang Plain were the main controlling factors for the changes in the vegetation carbon storage.