Eco-province, eco-city and eco-county construction programs started in China in 2000, and since then, there have been more than 15 provinces including Fujian, Hainan, Zhejiang, Jiangsu etc. completed eco-province construction planning. Scientific and effective indicator system is an important tool to carry out the assessment, planning and management of regional ecological construction. However, some problems still exist in the construction of ecological indicator system, such as lack of systematic study on the essence of the indicator and subjective process of indicator selection, which severely impair the science and validity of the ecological indicator system. An objective and scientific process of selection supplies the way for fast ecological construction planning and its adjustment in the future. This paper combines the network analysis and quantitative selection of indicators to build an ecological indicator system based on the previous practice in Fujian Province. We (1)analyzed the main problems existed in the ecological construction, implementation and development process, summarized the previous assessment indicators in the current ecological construction, studied the targets of Fujian eco-province construction practice, and established theme-oriented eco-province construction assessment network indicator system which contained 4 hierarchies and 55 concrete indicators representing experts and stakeholders' opinions; (2)identified the relationships among the indicators at the same or different hierarchies through the analysis of the cause-effect relationship, ecological processes and management requirements, and transformed them into an ecological hierarchy network (EHN) framework and assigned the weights of all the indicators based on the hierarchical structure and complex linkages of the EHN framework; (3)established indicator selection standard matrix which included measurable, vulnerable, predictable, typical, controllable, integrative, responsive, and stable criteria and built alternative indicator matrix of assessment system for ecological construction according to the scientific and efficient application standards of ecological indicator; (4)built a multi-objective selection model concerning socio-economic costs and ecological integrity and quantitatively select the ecological indicators system that is suitable for Fujian eco-province construction practice by genetic algorithm method. According to the selection results, at least 44 concrete indicators should be selected in the ecological construction assessment system of Fujian Province, 11 indicators were dropped out from the 55 alternative concrete indicators. The results showed that our research would be helpful for understanding the essence of the assessment indicator system of ecological province construction, improving the scientific and systematic level of indicator system construction, and enhancing the practicability of ecological indicator system for ecological construction assessment, planning and management. For the reason that it is hard to simulate the whole system by a purely mathematical model due to the limited understanding of complex ecosystem and social ecological system, it is suggested that the theme-oriented framework and network framework should be coupled with subjective and quantitative indicator selections for ecological construction practices of other provinces in China.