In the context of global climate change, the spatiotemporal characteristics of fractional vegetation coverage (FVC) serve as a crucial indicator for assessing ecological environment quality in various regions. However, the specific spatiotemporal variations, change trends, and underlying mechanisms of FVC response to human activities in Inner Mongolia remain undefined. Bridging this knowledge gap is essential for understanding ecological management outcomes and providing a scientific basis for local ecological policies and spatial planning. Using MOD13A1 NDVI data, land cover data, and nighttime light data spanning from 2000 to 2022, we calculated the annual maximum fractional vegetation coverage in Inner Mongolia and explored its spatiotemporal variations. Additionally, we illustrated the change trends in FVC. We conducted pixel-by-pixel correlation analysis to examine the response modes of FVC to human activities. Our findings reveal the following: (1) FVC distribution in Inner Mongolia demonstrated a decreasing trend from northeast to southwest, consistent with the overall precipitation changes in China. Notably, areas along the Yellow River, such as the Houtao Plain and the Qiantao Plain, exhibit relatively higher FVC due to abundant water resources and well-developed agriculture. Overall, FVC showed improvement with a growth rate of 0.0039·a^-1, remaining relatively stable in most areas (64.02%) and significantly increasing in 31.64% of the region, all prefecture-level cities showing a positive average annual growth. (2) Changing trends in FVC were predominantly nonsignificant (65.62%), followed by a significant increase (17.36%), an extremely significant increase (13.43%), a significant decrease (3.27%), and an extremely significant decrease (0.32%). Regions experiencing significant and highly significant reductions displayed a strong spatial correlation with newly developed construction land. (3) Regarding human activities in Inner Mongolia, most regions (79.67%) showed no significant influence on FVC changes. In 12.80% of the regions, human activities positively impacted FVC, primarily in grassland and arable land areas surrounding urban zones. Conversely, 7.53% of the regions demonstrated a negative impact of human activities on FVC, chiefly in areas undergoing land cover transitions from arable land to construction land and newly added industrial and mining zones. While most regions showed no significant correlation between FVC variation and human activities, this does undermine the impact of ecological protection policies implemented in China like the “Ecological Protection Red Line” and “Arable Land Red Line.” The effectiveness of these measures lies in preventing land type conversion, such as grassland and arable land to other categories. This not only maintains the stability of FVC within protected areas but also regulates the intensity of human activities. However, the outcomes of these measures are not adequately reflected in nighttime light data. Therefore, while nighttime light data partially reflect the influence of human activity intensity on FVC, its limitations must be fully recognized in the comprehensive evaluation of ecological protection policies.