Previous field observations have shown that NO3 and related species develop distinct vertical profiles in urban areas. In this study, we utilized the Platform for Atmospheric Chemistry and Vertical Transport (PACT) under observation constrains to simulate NO3 and related substances during field campaign in Beijing in the autumn of 2019. The simulations of NO3 for each layer have achieved a good agreement (R ≈ 0.92) with the LP-DOAS observations for the whole period. The vertical NO3 budget analysis concluded that direct loss dominates at the lowest layer (over 70%), while indirect loss is most significant at the upper layer. But what we found in this study is that direct NO3 loss is not only confined to the ground, but also has a vital proportion of 50% at high altitudes. What's more, case study of fast NO3 decay situation (Case II) shows that sometimes direct loss in the highest layer can account for more than 90% of the total NO3 loss, while indirect loss is more significant in the lowest layer than in the highest layer. In contrast, the poor NO3 simulation (Case III) indicates that the NO3 loss in the highest layer was all occupied by indirect loss. Loss pathway of NO3 in the high altitudes can be completely occupied by direct loss or indirect loss respectively, showing the complexity of the NO3 loss path. The sensitivity test on indirect NO3 loss rates via N2O5 heterogeneous reaction at highest layer suggested the importance of chemical equilibrium between NO3 and N2O5 on the budgets.