Photonic management is a key issue for the optimization of thermophotovoltaic (TPV) energy conversion systems. It is realized by selective emitters, front surface filters on TPV cells, and back surface reflectors (BSRs). Photonic management modifies photon energy transfer from the emitter to the TPV cell due to photon reuse and energy conversion processes in the TPV cell due to photon recycling and trapping in the cell. Our work has developed a comprehensive thermodynamic theory of photonic management in the TPV cell and in whole TPV systems to elucidate key optimization parameters. Our approach is based on the exact Lambert function solution of the generalized Shockley–Queisser model and the corresponding fundamental formulas of endoreversible thermodynamics for maximal electric power, emitted optical power, and dissipation losses. The model includes interrelated processes of photon recycling, photon trapping, nonradiative recombination, and parasitic absorption of the BSR. Optimization of a TPV system with photon reuse should take into account that the cell thickness that provides maximal output power does not correspond to the thickness, which gives the maximal conversion efficiency. The theory predicts the important limits for TPV efficiency and output power determined by the Auger recombination in low-bandgap semiconductor materials, various parasitic losses in the cell and conductive layers, and photon escape from the TPV system. For example, we consider the TPV system based on 0.6 eV InGaAs cells with a BSR and a front surface photon scattering layer, which provides Lambertian light trapping.