To explore the effects of nitrogen reduction combined with zinc fertilizer on root growth and development，carbon and nitrogen metabolism，yield and quality of tobacco in Chongqing tobacco area，a field experiment was carried out with ‘Yunyan 116’ as the test material，and a two-factor and two-level experiment was set up with nitrogen fertilizer (N1:conventional fertilization，N2:conventional fertilization with nitrogen reduction of 8%) and zinc fertilizer (Zn1:0 kg/hm²，Zn2:15 kg/hm²). The effects of different combined application of nitrogen and zinc on root morphological characteristics (root hair ultrastructure and root number)，physiological characteristics (root activity，soluble sugar and total nitrogen content，key enzyme activity of nitrogen metabolism)，main chemical components and yield of tobacco leaves were analyzed. The results showed that there were significant differences (P<0.05) in the number of adventitious roots，root activity，root total nitrogen content and nitrate reductase activity among different nitrogen and zinc combined application treatments. Under the condition of conventional nitrogen application with zinc fertilizer application，the number of tobacco root hairs and the number of roots increased gradually. The application of zinc fertilizer significantly improved the root physiological characteristics. Suitable nitrogen and zinc application is beneficial to the increase of tobacco root number，root physiological characteristics，main chemical composition and yield. The yield of flue-cured tobacco leaves in N1Zn2 treatment was the highest (2074.66 kg/hm²)，and the output value was the highest (48982.72 yuan/hm²). The main chemical components were more coordinated than other treatments. Considering the morphological and physiological characteristics of tobacco roots and the main chemical components and yield of flue-cured tobacco leaves from the interaction of nitrogen and zinc application，the selection of appropriate nitrogen and zinc application is not only beneficial to improve the yield of tobacco leaves，but also to achieve the ideal quality of flue-cured tobacco leaves. It is concluded that the most suitable fertilizer application amount under the condition of nitrogen and zinc combined application is:conventional nitrogen application of 90 kg/hm² with zinc application of 15 kg/hm².