The work is aimed at selection criteria determination applied to the appropriate components of apple tree orchard ecosystem ensuring its sustainable operation under conditions of southern Russia weather anomalies. The research has been carried out in apple tree cultivation areas at the educational-experimental farm “Kuban” of Kuban State Agrarian University in 2021–2024. The soils of experimental farms are leached chernozems. A sustainable orchard ecosystem creation is related to the use of a set of effectively interacting components within the framework of a complex “plant—microbial cenosis—soil”. The most important selection criteria for such components within specific natural conditions of southern Russia are some biological characteristics of a plant body. They include, in particular, special aspects of natural spring and late summer fruit drop, peculiar to a certain variety of apple trees as well as the ability of herbs used in the rows of cultivation areas to adapt to the soil and climatic conditions of relevant territories. The raising amount of a fungus Aspergillus in fungal cenosis of leached chernozem is associated with increase of apple trees resistance to water deficiency. On totality of the data obtained, the level of stability of organic orchard ecosystem is higher than an intensive one. It is necessary to use some regulatory mechanisms to increase operational effectiveness of an intensive orchard ecosystem under conditions of various summer weather anomalies.