As a small-scale renewable energy source, micro-hydropower can substitute fossil fuel to relief the energy shortage and acquire comprehensive benefits for the society, ecology as well as economy in mountain areas. However, the development and promotion of micro-hydropower are constrained by inferior management level and limited understanding on its benefits, of which only direct economic benefit is considered. This paper developed a comprehensive management information system for micro-hydropower using Visual C# and Access. The system was divided into four modules (data query, data editing, evaluation & analysis, plus planning & design) for three kinds of users (managers, investors and users). Specifically, the evaluation & analysis module is developed via analytic hierarchy process (AHP), which decomposed the module into five layers, namely the target layer, sub-target layer, criterion layer, index layer and index factor layer, where twenty nine index factors were employed to deliver an objective evaluation. In the planning & design module, the system offers a useful sub-module for optimal pipe diameter selection. In addition, the system covers a wide range of target users. For top managers and professional users, the system leaves plenty of room to perform analysis and evaluation for strategic decisions; for investors and users with limited professional knowledge, the system transforms the complicated mathematical model into simple parameter selection and delivers the optimal evaluation results in a user-friendly way for easier understanding. The study also reveals the power of management information system in the energy engineering filed.