The increase in nitrogen emissions has intensified environmental pollution, posing a serious threat to the sustainable development of human society. Nitrogen emissions originate from multiple sectors and products, generating various nitrogen species. However, existing studies have mostly focused on these nitrogen species individually, lacking a comprehensive analysis and interpretation. Here, we have integrated six different nitrogen species into a comprehensive indicator, namely overall nitrogen emissions. This study constructs a comprehensive emission inventory for 24 different products in 9 cities in the Pearl River Delta region of China from 2012 to 2021. Additionally, we use the index decomposition analysis (e.g., the Logarithmic Mean Divisia Index, LMDI) to analyze the main socioeconomic driving factors of overall nitrogen emissions in the Pearl River Delta over the decade (e.g., emission intensity, population, and affluence). We observed that Guangzhou has had the highest overall nitrogen emissions, reaching 4.24 Tg N, accounting for 27.64% over the past decade. Furthermore, overall nitrogen emissions in the Pearl River Delta have increased by 30.11%, from 1342.19 Gg N year−1 in 2012 to 1746.37 Gg N year−1 in 2021. Energy products are the primary contributing source to overall nitrogen emissions, followed by industrial and fertilizer products. Moreover, decomposition analysis results indicate that emission intensity is the main factor driving overall nitrogen emission reduction in the Pearl River Delta over the decade. However, affluence and population show a positive correlation with overall nitrogen emissions, offsetting the nitrogen reduction effect of emission intensity. Over time, the nitrogen reduction effect of emission intensity will gradually weaken, while the nitrogen increase effect of affluence and population will gradually strengthen. Our study highlights the importance of continued efforts to reduce emission intensity, while also transitioning towards non-nitrogen-intensive sectors or products in future economic development, thereby decoupling overall nitrogen emissions from affluence and population.