Algae-based aviation biofuel shows the potential to reduce soot emission in flight. A comparison study of soot precursor and aggregate property between algae-based biofuel and aviation kerosene RP-3 in laminar flame was conducted to investigate the reason of biofuel’s less soot formation. The soot precursors were determined by the fringe lengths of soot particles. At a typical dimensionless height DH = 0.50 of both flames, the geometric mean fringe lengths of biofuel and RP-3 are measured to be 0.67 and 0.73 nm, respectively, approximating to the size of five-ringed (A5) and seven-ringed (A7) poly-aromatic hydrocarbon, respectively. An A5 growth mechanism was then added to biofuel surrogate mechanisms for soot formation simulation. Since the carbon number component of biofuel is wide and difficult for comprehensive mechanism development, two surrogate mechanisms were developed. One is based on the C8–C16 n-alkane that covers biofuel’s main components, and the other one is based on biofuel’s average carbon number to simplify the mechanism. Meanwhile, an A7 growth mechanism was added to a popular RP-3 mechanism. The soot formation simulation with the combination mechanisms for both fuels provides a better agreement with the measured primary particle diameter and suggests that the reason for less soot production by biofuel is its less soot precursor production that weakens soot nucleation and growth. Lastly, the soot fractal dimension of biofuel is smaller than that of RP-3, indicating that biofuel has a looser soot aggregate.