Eco-compensation should be given to farmers in order to promote the Globally Important Agricultural Heritage Systems (GIAHS) for a higher level of eco-services. However, differences in farmer's livelihood endowments and strategies can directly affect the initiatives of their participation in compensation policies, resulting in different effects of these incentive policies. In order to improve the efficiency of eco-compensation policies, this paper takes Zhejiang Qingtian Rice-fish Culture System (RF) and Yunnan Yuanyang Hani Rice Terraces System (RT) as examples and adopts the canonical correlation mode to analyze, from the perspective of the heterogeneity of livelihood endowments, the impacts of farmers’ livelihood endowments on their participation in eco-compensation policies. The results showed that: (1) Cash compensation of the GIAHS eco-compensation program is a more popular method among farmers. The higher the comprehensive quality of the farmers is, the more acceptable the compensation polices will become and the higher their initiatives will be to participate in GIAHS conservation and agricultural production; (2) Land capital is a key positive factor influencing the satisfaction of the compensation policies of non-agricultural households and households with concurrent business. Human capital, on the other hand, is a negative factor influencing the initiatives of farmers’ participation in the GIAHS conservation. (3) The material capital in the R-F will improve farmers’ policy satisfaction, while financial capital and social capital can best affect the farmers’ initiatives to participate in the GIAHS conservation. (4) The land capital and material capital in the R-T affect farmers’ policy satisfaction. Material capital is also a positive factor influencing the initiatives of agricultural conservation.