Huai river basin has entered into green development dilemma with slowing down economy and severe environmental pollution. This paper, based on green development theory, discusses the features of this dilemma from ecological efficiency, and combined with development history and situation of Huai river basin, and studies theoretically the conducting mechanism. Malmquist index is used to measure its ecological efficiency. It is concluded that a low ecological efficiency contributes to the green development dilemma. Panel data model is applied to analyze the factors of low ecological efficiency. Resource industries play a critical role to others. Adjustment of single industry or some factors can not resolve the dilemma. Huai river basin should begin from laws, optimizing industrial structure and scientific talents, promote technical advances and increase ecological efficiency so as to resolve the green development dilemma.