Transferring biomass-derived cyclic ketones like cyclopentanone and cyclohexanone to mono-condensed product by aldol self-condensation has great potential in synthesizing renewable high-density fuel. But the selectivity is low for many catalysts due to the rapid formation of di-condensed byproducts. Herein, MIL-101 encapsulating phosphotungstic acid was synthesized to catalyze the self-condensation with selectivity over 95%. PTA clusters are uniformly dispersed in MOF cages and decrease the empty space (pore size), which provides both acidic sites and shape-selective capability. The optimal PTA amount decreases corresponding to the increase of reactant size. The shape-selectivity is also realized by changing the pore size of MOF, like from MIL-101 to MIL-100. Moreover, the catalyst is resistant to PTA leaching and performs stably after 5 runs. After hydrodeoxygnation of mono-condensed product, high-density biofuels with density of 0.867 g/ml and 0.887 g/ml were obtained from cyclopentanone and cyclohexanone, respectively. This work not only provides a promising way for high-density biofuel but also suggests the advantage of MOF-based catalysts for shape-selective catalysis involving large reactant.