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The development proccess in spatial term is always faced with a phenomenon called regional disparity. The emergence of this phenomenon shows the differences or unbalanced in development level, prosperity, Economic and spatial structures. Some regions achieves rapid growth, while other regions have experienced slow growth. Siak regency, particulary the central area of the capital city of Siak has experienced a rapid concentration of economic growth, while its hinterland in eastern part, has experienced very slow growth. The eastern region is getting slowly and weaker due to the exploitation of resources absorbed by the capital city of Siak, high urbanization to the city center, educated and skilled people aglomerated within city center, high protected of land, centralized economic activities in one place and low mobility of goods and services in eastern region in Siak Regency. This back wash effect makes the eastern region in Siak is left behind rather than city center. This study aims to develop a strategy to strengthen the institutional capacity to overcome regional disparity in Siak Regency. In this study, descriptive qualitative method are adopted by using institutional linkage analysis and scenario of institutional strengthen development by applying economic development and regional cluster concept. The result indicates that the institutional capacity in eastern region of Siak are still weak. This is proven by the assesment of ahievement which shows that most variables have not reach all the indicators. The role of institutional has not been integrated with the city development program, lack of coordination starting from planning, implementation and evaluation stages are still sectoral and high potential conflict of interest in Siak Regency. So, it takes a strategy to strengthen the institutional capacity through the scenario of development with economic development and regional cluster concept. The first stages is for establishment (year 2019 sd 2023) by doing revitalization of local economic and regional cluster, the second stages is for functionalizing (year 2024 sd 2028) with optimizing and stabilizing the function of institutional linkages, the third stages is for innovation (year 2029 sd 2038) by expanding the afinity and networking development scales to contribute to the enviromental preservation, the fourth stages is for suistanability (year 2034 sd 2038) with a sustain of institutional progress to contribute to the economic independence, enviromental suistanability and preservation of historical area.