Increasing human activities and climate change have resulted in significant changes in net primary production (NPP) of the marginal sea in the past several decades. The Bohai Sea (BHS) is a shallow semi‐enclosed marginal sea of North China, the knowledge of the relative impacts of human activities and climate change on the NPP in the BHS remains limited. This study primarily aimed to elucidate the interannual variability of NPP and its influencing factors in the BHS during the 2002–2021 period by synthesizing four widely‐used global NPP models, namely the vertically generalized production model (VGPM), the Eppley‐VGPM, the size‐fractioned phytoplankton pigment absorption‐based model (SABPM), and the carbon, absorption, and fluorescence euphotic‐resolving model (CAFE). The multi‐model average NPP showed significant interannual variation, with an increasing trend from 2002 to 2012 and a decreasing trend from 2012 to 2021. The concentration of DIN in the BHS was primarily affected by atmospheric nitrogen deposition. The structural equation model demonstrated that chlorophyll‐a (Chl‐a) concentration, influenced by DIN concentration, had an important effect on NPP. In brief, atmospheric nitrogen deposition impacted the DIN concentration and thus controlled the (Chl‐a) concentration and NPP change in the BHS. Furthermore, atmospheric nitrogen deposition in the BHS have potential ecological impacts on the red tide features. These findings hold valuable implications for future marine resource planning and marine ecological management in the BHS.