This article summarizes the results of the first phase of the study of sectoral and spatial transformations in the region economic system. Its distinctive feature is the focus on the analysis of intra-regional differences, including the study of the regional rural periphery structure. The article describes in details the situation in research in terms of changes in the territorial structure of the regional economy, studied at the cross-disciplinary level of regional economy, economic and social geography, urban and rural sociology, etc. The authors assessed the views of leading researchers of theoretical and methodological foundations development, the problems of economic space state regulation, territorial differentiation, as well as rural development and rural settlement. The article widely presents different approaches of domestic and foreign researchers to analysis and assessment of spatial development and territorial changes. The authors highlight the main directions in spatial analysis development and outline the approaches to the formation of a system of indicators and index of changes in the territorial structure of the regional economy.