Spirulina algae oil possesses high potency for biodiesel production through transesterification reaction. Fatty acids of Spirulina algae oil were derived and identified by gas chromatography-mass spectroscopy (GC-MS) technique included Palmitoleic acid, Palmitic acid, Linoleic acid, Margaric acid, Oleic acid, Arachidic acid, Behenic acid, Tricosanoic acid, and Lignoceric acid. In this research, [Cu(H2PDC)(H2O)2] complex was synthesized using of 2,6-pyridinedicarboxylic acid ligand via a hydrothermal method. [Cu(H2PDC)(H2O)2] has been identified using techniques such as single crystal X-ray diffraction (SXRD), X-ray powder diffraction (PXRD), Scanning Electron Microscopy (SEM), Thermo gravimetric Analysis (TGA) and infrared spectroscopy (FTIR). In parallel, the electronic structure, net atomic charges and HOMO/LUMO analysis are interpreted using density functional calculations for studied compound. In continuation, the transesterification reaction of Spirulina algae oil with methanol was performed to produce biodiesel using Cu(H2PDC)(H2O)2 complex. The operating conditions of the reaction, including, temperature, methanol to oil ratio, and catalyst content were checked and screened. The observed results indicate that [Cu(H2PDC)(H2O)2] complex acts as a suitable catalyst for transesterification reaction of Spirulina algae oil with 98.45% conversion percent under reaction conditions 0.15 g catalyst, algae oil-to-methanol volume ratio of 1:3, reaction temperature 80 degrees C, and 48 h.