Green energy production connected with global warming is one of the hottest topics for industry, technology, and life science. Microalgae culture and its potential for industrial applications in CO2 fixation from flue gases for second generation biofuels and many other valuable metabolites’ production has received much attention in recent years. The goal of this review is to combine all the key knowledge obtained in state of the art studies in recent years about the modeling of photobioreactors (PBRs). In order to develop the complex PBR phenomenological model, we considered it as a system and applied the theory of system analysis on PBR. Special attention was given to decomposition principles of this theory where the PBR system was divided into sub-systems. Furthermore, this review shows how to combine the knowledge from modeling of sub-systems by taking into account relationships between them, and how such interrelationships influence the overall PBR modeling procedure for the particular microalgal cultivation process. The result of this work is a successful development of a complex PBR phenomenological model, which was presented as an independent original authors’ work.