A principle of hierarchical entropy maximization is proposed for generalized superstatistical systems, which are characterized by the existence of three levels of dynamics. If a generalized superstatistical system comprises a set of superstatistical subsystems, each made up of a set of cells, then the Boltzmann-Gibbs-Shannon entropy should be maximized first for each cell, second for each subsystem, and finally for the whole system. Hierarchical entropy maximization naturally reflects the sufficient time-scale separation between different dynamical levels and allows one to find the distribution of both the intensive parameter and the control parameter for the corresponding superstatistics. The hierarchical maximum entropy principle is applied to fluctuations of the photon Bose-Einstein condensate in a dye microcavity. This principle provides an alternative to the master equation approach recently applied to this problem. The possibility of constructing generalized superstatistics based on a statistics different from the Boltzmann-Gibbs statistics is pointed out.