Ordered mesoporous carbon based catalyst (MCC catalyst) derived from microalgal waste biomass was prepared through condensation and hydrothermal post-treatment process at 90 °C and 120 °C, respectively. Biochar obtained from pyrolysis of the waste was sulfonated in concentrated H2SO4 solution at 150 °C for 15 h to introduce sulfonic groups to the biochar’s structure consisting of condensed polycyclic aromatic rings. This process modified biochar to sulfonated biochar (SBP) which was then applied as precursor in the MCC catalyst preparation. The MCC catalyst structure was demonstrated for its ordered mesoporous structure. The thermal behavior of the catalyst was then investigated by heating process with and without using oxygen for estimating its thermal stability. The acidity of the catalyst was also considered through propylamine-TPD established in TG–MS machine. The catalysts activity was tested in conversion of linseed oil to methyl ester under mild conditions of 120 °C for 3.5 h, and the yield of methyl esters was up to 94.6% proving its high activity and selectivity in the conversion. In this study, TG–DSC coupled with MS, XRD, TEM, NH3-TPD, BET-BJH, techniques were applied to characterize the catalyst, and GC–MS was used for determining the methyl ester composition of the product.