The oxygenic photoautotrophs, cyanobacteria, possess vital biochemical pathways in their metabolism that enable them to fix atmospheric CO2 and synthesize a variety of metabolites. Nevertheless, the economic viability of cyanobacteria-based biofuels poses a barrier, prompting the development of various strategies to enhance the production performance of these microorganisms. The creation of bioengineering methods has made it possible to manipulate cyanobacterial metabolic pathways to produce a range of valuable bioproducts through photosynthetic processes. The efficient use of cyanobacteria as photosynthetic cell factories requires a thorough comprehension of their metabolism and how it interacts with other cellular processes. The application of systems and synthetic biology tools has produced a lot of data on various metabolic pathways. However, to create effective engineering strategies for additional growth, photosynthetic efficiency, and increased production of target biochemicals, a thorough understanding of their carbon/nitrogen metabolism, pathway flux distribution, genetic regulation, and integrative analyses is needed. The field of systems biology and genomics has led to the recognition of a new paradigm in systems metabolic engineering. Specifically, a systems-based approach essential for whole-cell inquiry and prediction is a reconstruction and modeling of the genome-scale metabolic network. To highlight our present understanding of cyanobacterial metabolism, we address recent developments in integrative modeling techniques and omics investigations (genomics, metabolomics, transcriptomics, and proteomics) in this chapter.