Implementation of the Grain for Green program (GGP) resulted in great changes in land use and cover in northwest China, and presumably in the region's carbon. However, accurate assessment of the effects of the GGP on carbon storage remains a challenge. The Integrated Valuation of Ecosystem Services and Tradeoffs (InVEST) model can map and evaluate natural goods and services that sustain life and quantify their impact from the changes in the ecosystem. Taking Huining County in China's Loess Plateau region as a case, the land use and land cover changes (LUCC) following the GGP were quantified, and their effects on carbon storage between 2000 and 2016 were evaluated using the InVEST model. The results showed that, a total area of about 3996.13 km2 underwent changes following the GGP in Huining County during the study period, accounting roughly for 74% of the county. The total carbon storage increased from 6470.72 Gg in 2000 to 7335.07 Gg in 2016. Spatially, carbon density in the south of this county was greater than the northern part. Directly induced by the GGP (conversions of farmlands to forests and grasslands), the carbon storage increased by 786.84 Gg in total, with a rate of 46.28 Gg per year, the majority of which occurred during the first stage of the study period (from 2000 to 2008). The increase of carbon storage was mostly attributable to the increases in vegetation pool and the carbon density showed a strong spatial correlation with the growing season Normalized Difference Vegetation Index (NDVI). The similarities between carbon density and NDVI spatial patterns during the study period may have been shaped by the county's climate patterns, but not to any significant extent by climate change during the study period. This county-scale study allows for a deeper understanding of the links between LUCC induced by environmental restoration programs and carbon storage changes, and contributes to a greater accuracy in the estimation of carbon storage at the provincial (or larger) scale. •Land use changed significantly with implementation of the Grain for Green Program in Huining County.•Carbon storage greatly increased with land use change, from 6470 Gg in 2000–7335 Gg in 2016.•Vegetation pools played a major role in increases of carbon storage.•Preventing conversions of forests and grassland to farmlands can improve the carbon sequestration effects of the GGP.•This study can contribute to the accurate estimation of carbon storage at a provincial or wider scale.