Transition metal oxides (TMOs) are widely employed in electrochemical energy conversion, yet their surface structures are prone to degradation and reconstruction under operating conditions, which significantly undermines catalytic stability and service life. In this work, we systematically investigate the coupling relationship between surface oxygen vacancy configurations and catalytic activity/structural stability in β-MoO3 during the nitrogen reduction reaction (NRR). Our results reveal that specific oxygen vacancies, such as the OVS-3 type with undercoordinated Mo centers, markedly enhance N2 adsorption and facilitate the initial hydrogenation step, thereby enabling more favorable NRR pathways. However, ab initio molecular dynamics (AIMD) simulations show that these highly active configurations are thermodynamically unstable and prone to surface reconstruction, leading to the deterioration of active sites. To address this activity–stability trade-off, we propose a single-atom doping strategy by incorporating transition metals such as Cr and W near the vacancy sites. First-principles calculations demonstrate that such doping not only preserves the desired electron structure for NRR but also significantly improves the thermal stability of the catalyst surface. Furthermore, the doped systems exhibit enhanced selectivity toward NRR by effectively suppressing the competing hydrogen evolution reaction (HER). Our study demonstrates that surface oxygen vacancies on β-MoO3 play a dual role: they enhance nitrogen adsorption and reduce the reaction barrier in the nitrogen reduction reaction (NRR) but also lead to surface reconstruction and catalytic site deactivation under operating conditions.