Abstract: An improvement in rice planting mode is important to reduce costs and increase production efficiency and grain income in hilly areas. Compared with artificial planting mode, machine-transplanted seedlings and direct seeding modes are more efficient, and they improve the economic benefit of rice production. However, their high material and energy requirements impose pressure on the ecosystem to a certain extent. Therefore, an evaluation of the sustainability of different rice planting modes in hilly and mountainous areas from a comprehensive cost-benefit and ecological economic perspective is of great significance for green and high-quality development of the rice industry. In this study, different planting modes of single mid-season rice in Yongchuan District of Chongqing City, which is an advanced county for national grain production in China, were evaluated. Cost-benefit and emergy analyses were conducted to compare the main production processes, net benefits, emergy structure, and investment in artificial planting mode, mechanical transplanted seedling mode, and direct seeding mode; and their ecological sustainability was quantitatively evaluated based on agro-environmental, emergy economic, and sustainability indexes. The results showed that there were differences among three planting modes in their main production processes, material and labor inputs, yield, and economic output. The direct seeding mode had the highest rice yield, followed by the mechanical transplanting seedling mode, and then the artificial planting mode. From the cost-benefit perspective, the benefits of the three planting modes were low or even at a loss and their economic sustainability was weak. In terms of cost composition, the cost of materials and services was the highest, accounting for 37.92%–48.52% of the total cost. The second highest was land rent, accounting for 35.78%–42.63% of the total cost. Labor inputs accounted for 9.09%–26.30% of the total cost, and this variation was an important factor affecting the profitability of mid-season rice production when different planting modes were used. Emergy structure analysis showed that the renewable resource input and non-renewable environmental resources of the three rice planting modes were the same, whereas the supplemental emergy input was different and in the following order: machine-transplanted seedling mode > artificial planting mode > direct seeding mode. Industry supplemental emergy input was the main input form, of which fertilizer input and rice drying emergy consumption were the main components, accounting for 49.00%–56.54% and 27.32%–32.74% of industrial supplemental emergy, respectively. To improve the sustainability of different rice planting modes, methods for efficient fertilizer utilization and rice drying emergy reduction should be further explored. The results of the agro-environmental indexes showed that the pressure on the agro-ecological environment by the three planting modes was low. The results of the emergy economic indexes showed that the emergy investment-to-yield ratio of the direct seeding mode was better than that of the other two modes. Emergy sustainability index indicated that the three types of rice systems mainly depended on the input of environmental resources and were natural resource-driven eco-economic systems. Overall, the direct seeding mode had the greatest economic and ecological advantages, and can be further promoted and applied in hilly areas. Planting mode improvement methods should be fully explored to maintain healthy development of regional rice production. Planting mode improvements are important measures for reducing investment costs and increasing production efficiency and grain income in hilly areas.