Some countries, including Taiwan, have adopted strategic environmental assessment (SEA) to assess and modify proposed policies, plans, and programs (PPPs) in the planning phase for pursuing sustainable development. However, there were only some sketchy steps focusing on policy assessment in the system of Taiwan. This study aims to develop a methodology for SEA in Taiwan to enhance the effectiveness associated with PPPs. The proposed methodology comprises an SEA procedure involving PPP management and assessment in various phases, a sustainable assessment framework, and an SEA management system. The SEA procedure is devised based on the theoretical considerations by systems thinking and the regulative requirements in Taiwan. The positive and negative impacts on ecology, society, and economy are simultaneously considered in the planning (including policy generation and evaluation), implementation, and control phases of the procedure. This study used the analytic hierarchy process, Delphi technique, and systems analysis to develop a sustainable assessment framework. An SEA management system was built based on geographic information system software to process spatial, attribute, and satellite image data during the assessment procedure. The proposed methodology was applied in the SEA of golf course installation policy in 2001 as a case study, which was the first SEA in Taiwan. Most of the 82 existing golf courses in 2001 were installed on slope lands and caused a serious ecological impact. Assessment results indicated that 15 future golf courses installed on marginal lands (including buffer zones, remedied lands, and wastelands) were acceptable because the comprehensive environmental (ecological, social, and economic) assessment value was better based on environmental characteristics and management regulations of Taiwan. The SEA procedure in the planning phase for this policy was completed but the implementation phase of this policy was not begun because the related legislation procedure could not be arranged due to a few senators' resistance. A self-review of the control phase was carried out in 2006 using this methodology. Installation permits for 12 courses on slope lands were terminated after 2001 and then 27 future courses could be installed on marginal lands. The assessment value of this policy using the data on ecological, social, and economic conditions from 2006 was higher than that using the data from 2001. The analytical results illustrate that the proposed methodology can be used to effectively and efficiently assist the related authorities for SEA.