Aldol condensation is a key step for converting the lignocellulosic platform compounds to fuel. The catalyst used in the aldol condensation requires the avoidance of the overactivation of aldehyde groups while fully activating ketone carbonyl groups. Herein, the modified chitosan (NaOH/CT-0.6) was applied for the efficient syntheses of single condensation product from biomass-derived furfural (FFR) and methyl isobutyl ketone (MIBK), achieving an 87.01% yield of C11 at 60 °C and 3 h. Catalyst characterization revealed that the exposure of –NH2 groups in chitosan after modification led to the formation of the imine with the CO groups of FFR. It was confirmed that the imine formation avoided the overactivation of aldehyde groups and improved cross-condensation product yield. Furthermore, the theoretical feasibility of the imine catalytic path was elucidated through DFT simulation and in situ DRIFTS analysis. Finally, the obtained condensation products were subjected to hydrodeoxygenation (HDO) over the 2 wt% Pd/Nb2O5, obtaining the hydrocarbon components suitable for bio-jet fuels. This work contributes significantly to the design of novel catalysts for aldol condensation reactions and the efficient conversion of biomass.