The problem of developing rural areas has existed in Russia since the beginning of market reforms, and it has not been fully resolved. Sustainability in the theoretical sense is achieved with the ability of rural areas to develop even under the influence of negative external factors, development is determined by the achievement of significant results for local communities. Stability can also be described by mathematical criteria, which forms the basis of the proposed methodology. It includes several stages, initially a quantitative description of the characteristics of the development of rural areas, the most significant in the development of local communities, is formed. Evaluation of stability indicators by a series of dynamics makes it possible to single out a “key” trend, which is understood as a negative trend in the development of rural areas, which is the most significant problem for them. Its resolution corresponds to a radical change in trends, corresponding to the transition to sustainable development, which can be described using a trend model, the refinement of which based on the sequence of impacts on the conditions of rural development, provides a more reasonable assessment of the indicators of sustainable development of rural areas. The possibilities of the methodology are demonstrated on the example of the Novosibirsk region, where the “key” trend is associated with a steady decline in the rural population. Given an assessment of the parameters of this indicator in the case of a transition to sustainable rural development, the substantiation of some other characteristics of the development of rural areas of the Novosibirsk region is presented. The proposed methodology can be used to establish indicators for target programs focused on the development of rural areas in the regions.