In this paper, a Petri net-based model of the fluorescence of the nicotinamide adenine dinucleotide (NADH) and flavin adenine dinucleotide (FADH2). NADH and FAD nucleotides from the electron transport chain and the swelling of isolated mitochondria is presented. The model describes selected aspects of these processes under the influence of the chosen electron transport chain chemical modificators. The model expressed in the language of the Petri net theory has an intuitive graphical interpretation and can be analyzed using rigorous mathematical methods. For the simulation experiment, we chose the Cell Illustrator v.3 software (Human Genome Center, University of Tokyo, Japan). An analysis of the fluorescent response of NADH/FAD in the isolated mitochondria to specific electron transport chain inhibitors (rotenone, antimycin A, and sodium cyanide (NaCN)) and protonophore carbonyl cyanide 3-chlorophenylhydrazone (CCCP) revealed a correlation between the changes in the NADH/FAD fluorescence (their redox state) and the functions of particular complexes in the inner mitochondrial membrane. The inhibition of the electron transport chain resulted in the organelle’s swelling; we obtained mathematical equations through modeling to formalize the process of mitochondria swelling and NADH/FAD fluorescence changes in a medium with sodium azide. In particular, these equations adequately and simultaneously described the time characteristics of the reduction of the fluorescence of nucleotides and the swelling of mitochondria. Our model enabled us to predict the changes in the organelle NADH/FAD fluorescence and their hydrodynamic diameters in time. Furthermore, it helped us to optimize the experimental procedures, allowing us to analyze the process dynamics and to compare the modeling results with actual observations under changing compositions of the incubation media and the presence of activators/inhibitors.