Nitrogen (N) is an essential element for food production. Under the influences of correlated variables of food demand and socio-economic development, a hybrid approach was proposed to identify reactive nitrogen (Nr) loss from livestock-based food and biofuel production systems. The approach included the following components: (1) crop simulation model, DeNitrification-DeComposition, taking into account several field situations and climate change scenarios, and (2) correlation analysis of five types of livestock-based food demand and economic benefits based on copula functions and Markov Chain Monte Carlo simulation. The approach was applied to the Guangdong–Hong Kong–Macao Greater Bay Area (GBA) in China. Production of fodder crops (maize, wheat and soybeans) was examined under two climate change scenarios, Representative Concentration Pathways 4.5 and 8.5. Influence of international trade of soybeans, wheat, and maize on nitrogen fertilization was examined under two additional scenarios. Results showed that compost production from livestock manure and food loss in the production of 1000 kg of livestock-based food would reduce demand for 10.45 kg of urea in crop production, accounting for 9.2%–14.66% of total nitrogen fertilizer demand. Among all livestock-based food, fertilizer demand between 2020 and 2030 is projected to be the highest in fodder crop production to support pork production. Total Nr loss of livestock-based food production in GBA was estimated to be 1.10 to 1.58 Mt under scenario 1, and 1.09 to 1.57 Mt under scenario 2.