The greenhouse gas (GHG) emissions from agriculture, forestry, and other land use (AFOLU) account for more than 10% of the total GHG emissions in Iran. To reduce the environmental impact, assessments of Iran’s GHG emissions status are critical for identifying the national policies to achieve Sustainable Development Goals (SDGs) in the bio-based industry. However, there is no study exploring the dependency between AFOLU and GHG emissions in Iran by using the Vine Copula approach. Hence, the study aims to examine the causality direction and correlation structure among selected horticulture, farming crops, livestock, and poultry products and carbon dioxide (CO2), nitrogen dioxide (N2O), and methane emissions (CH4) in the Iranian agriculture sector over the period 1961–2019, to determine which crops or products are more responsible to deteriorate the environment. The empirical strategy used a C-Vine Copula model to measure the correlations together with the Granger causality (GC) test to analyze the causality links. According to the empirical findings, several crops and products are the sources of emissions. Rice and vegetable cultivations, as well as meat and milk products (Kendall’s τ values of 0.37, 0.33, 0.31, and 0.31, respectively), are the leading sources of CH4 emissions. Legumes, eggs, maize, rice, and milk enhance N2O emissions, while CO2 emissions are caused by apple, potato, and apricot crops (Kendall’s τ values of 0.22, 0.18, and 0.16, respectively). Finally, based on the findings, policy implications are offered.