The article highlights the problems of heterogeneity and dissociation of the economic space of Russia, the lack of effective interaction of territorially localized systems. The solution of these problems is possible on the basis of constructing the activity of planning subjects within spatial social and economic systems considering influence of factors of environment uncertainty, their quality, complexity and high dynamism. Strategic planning of the development of spatial socio-economic systems involves the study of the external environment to identify opportunities and threats, define their strengths and weaknesses and competitive advantages, formulate the mission and development goals, and choose a strategy to achieve them based on the analysis of alternatives. Algorithms for working out a program for regional socio-economic development and a program for socio-economic development of the municipality have been proposed. The organization of the process of creating the regional socio-economic development program in accordance with the proposed algorithm will significantly increase the efficiency of planning, interaction between authorities and society; it will allow a sufficiently high level of detail, excluding contradictions, to coordinate the priorities of balanced and sustainable development of individual regions and the region as a whole. The inclusion in the planning processes the spatial and socio-economic development of the region and its municipalities allows to ensure compliance with the principle of the unity of spatial and socio-economic planning, which is an undoubted advantage of the algorithms proposed. The analysis of the existing regulatory framework on the problems of strategic planning of spatial and socio-economic development of the Astrakhan region has been given. It is recommended to make certain adjustments to the law on regional strategic planning of the Astrakhan region. It has been inferred that synchronization of the process of strategic planning of spatial and socio-economic development of spatial socio-economic systems can be organized by eliminating the inconsistency of actions of power structures, local self-government and economic entities; improving the efficiency of management decisions of regional power structures and local self-government.