Ecological agriculture improves ecological environment and helps farmers earn more money. Its profitability plays a vital role for farmers to participate ecological agriculture. This paper, based on a case study on Wushan county, Chongqing, uses Cobb-Douglas model to analyze the influence of land endowment, external environment and farmers on profitability of ecological agriculture. Profitability will decrease if the ratio of slope farmland to flat dam land is over a certain limit. Profitability will decrease if farmland is fragmented, but it will increase through land consolidation if farmland is too fragmented. The higher rate of land rocky desertification, the lower profitability. Traffic costs and aged farmers significantly reduce profitability. Honeysuckle planting area is too small, far from achievement of scale efficiency. Market risks also decrease the planting profitability, which can be largely increased if farmers can get financed and technical supports.