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Irrigation improvement has been identified as an important adaptation strategy for the food and water security under climate change. Ecological and economic feasibility analysis of irrigation improvement projects is of vital importance to ensure the high investment efficiency and the sustainability of irrigation development. This study integrated emergy, economic and sensitivity analysis methods into a combined analysis. A case study on a small-scale irrigation project in plain areas of Jiangsu Province in China illustrated the methodology. The results indicated that different calculation results were obtained by using emergy and economic analysis methods, respectively. The conventional monetary based analysis method could underestimate or overestimate the assessment indicators. Emergy as an eco-centric method could neglect the economic utility, human preference and demand. Economic analysis and emergy accounting as the complementary valuation methods should be jointly used to provide better insights into the environmental and economic effects of irrigation improvement projects.