Abstract: Chongqing City is an important agricultural development area, and many agricultural inputs are used in agricultural production activities. Carbon emissions are generated during the use of agricultural resources. Analyzing the characteristics and influencing factors of carbon emissions of agricultural inputs in Chongqing City is vital for green agricultural development and promoting the achievement of the “dual carbon” goals. The number of agricultural inputs, grain output, cultivated land area, sown area, rural population, and various GDP values of Chongqing City were integrated based on the Chongqing Statistical Yearbook and China Agricultural Yearbook for 2013–2022. Classical carbon emission calculation theory was used to study the carbon emissions of inputs and their dynamic changes in agricultural production in Chongqing City from 2013 to 2022. The logarithmic mean divisia index (LMDI) and Tapio decoupling models were used to explore the influencing factors and decoupling effects of agricultural input carbon emissions, providing scientific support for agricultural input carbon reduction. The results were as follows. 1) In the past 10 years, the amount of agricultural inputs in Chongqing City showed an increasing trend before 2015 and a decreasing trend (apart from compound fertilizer) after 2015. The total carbon emissions from agricultural inputs in Chongqing City have fluctuated within the range of 452.01×10⁴ to 482.70×10⁴ t CO₂-eq, and reached the lowest in 2021. Fertilizer and electricity for irrigation were the primary sources of carbon emissions of agricultural inputs, accounting for 31.01% and 39.48%, respectively. 2) Compared to the base period, carbon emissions per unit sown area, unit output, unit output value, and unit cultivated land area of Chongqing City showed downward trends, and the trend of carbon emissions per unit cultivated land area was consistent with that of carbon emissions per unit sown area. 3) Both changes in agricultural inputs and planting structure affected agricultural input carbon emissions, whereas factors such as agricultural production efficiency, regional industrial structure, and rural population positively affected agricultural carbon reduction. The agricultural industrial structure, regional economic development level, and labor force level were the main reasons for the increase in carbon emissions of agricultural inputs in Chongqing City. 4) The decoupling state between carbon emissions from agricultural inputs and economic growth in Chongqing City mainly manifested as a transition from weak to strong decoupling. Agricultural economic growth has gradually eliminated the dependence on high carbon emissions, achieving relatively green development. The findings of this study provide recommendations for Chongqing’s decision-making on carbon emission reduction from agricultural inputs. The government should accelerate the research and development of green agricultural technologies, such as precision fertilization, water-saving irrigation, and intelligent equipment, adjust the structure of the agricultural industry, and promote the development of organic and ecological agriculture. Simultaneously, it is imperative to enhance farmers’ environmental awareness and low-carbon production capacity while curbing the carbon emission drivers associated with agricultural inputs.