Data envelopment analysis is an effective method for assessing the relative sustainability of ecosystems in megalopolises, which are characterized by a variety of environmental and socio-economic indicators. The existing models do not allow adapting the parameters of data envelopment analysis models to the preferences of the decision-maker and do not provide a consistent assessment of the effectiveness of complex socio-economic systems. The most important characteristics of complex socio-economic systems have to be calculated by indirect methods by solving a number of optimization problems. Adaptive data envelopment analysis models are developed to determine the sustainability of ecosystems in megalopolises on the basis of ecological and socio-economic indicators of anthropogenic load. In the proposed adaptive models, intermediate results at the previous stage of the functioning of the megalopolis ecosystem are only partially consumed at the next stage. A part of the input parameters of the functioning of the ecosystems of the megalopolis can be freely distributed. Additional input parameters are directly consumed at the next stage of the functioning of the megalopolis ecosystem. The optimal values of the parameters of the models are determined on the basis of the dialogue procedure of sequential cutting of multidimensional sets using affine subspaces. Indicators of sustainability of ecosystems of megalopolises, which characterize a low level of anthropogenic load, are calculated.