Vegetation net primary productivity (NPP) is a crucial indicator for assessing the carbon balance in terrestrial ecosystems. Qualitative and comparative research on the NPP influenced by human activities, climate change, and their interactions remains insufficient. The Three-North Shelter Forest Program (TNSFP), initiated in 1978, provides a valuable reference for such investigations. This study employs an improved residual trend method to analyze the spatiotemporal patterns, trends, and driving factors of vegetation NPP during the second phase of the Three-North Shelter Forest Program (2001–2020), as well as TNSFP’s contribution to vegetation NPP. The results indicate that (1) from 2001 to 2020, overall vegetation NPP exhibited a significant fluctuating upward trend at a rate of 3.69 g C/m−2 annually; and (2) precipitation, accounting for 1.527 g C/m−2, had a more significant impact on vegetation net productivity compared to temperature (0.002 g C/m−2). Climate factors (76%) significantly influenced vegetation NPP in the Three-North Shelter Forest region more than human activities (24%). In the last decade (2011–2020), the climate contribution rate decreased to 67%, while the human activity contribution rate increased by seven percentage points compared to the previous decade (2001–2010); (3) during 2001–2020, TNSFP contributed 10.9% to the total human activity contribution to vegetation net primary productivity, approximately 2.6% of the overall contribution; (4) After the second phase of TNSFP was enacted, PM2.5 levels decreased by an average of −0.57 μg/m−3/a−1. Concurrently, soil conservation improved from 6.57 t/km2 in 2001 to 14.37 t/km2 in 2020.