The development of acid-base catalysts for one-pot cascade reactions remains challenging because of the inherent incompatibility of inorganic acid and base active sites. Here, we introduced an innovative approach that employs spatial separation to construct separated inorganic acid-base sites, achieving sequence control of acid-base cascade reactions. The as-prepared bifunctional catalyst applied metal-organic framework (MOF) nanocrystals as spatial separators, with the inside microcavities loaded with 1 nm inorganic polyoxometalate acid H3PMo12O40 clusters (NENU-5) and the outside crystal surface covered with basic CuCo layered double hydroxide (CuCo-LDH) nanosheets. By applying the resultant NENU-5@CuCo-LDH catalyst to cascade deacetalization-Knoevenagel condensation, over 99% of the benzaldehyde dimethyl acetal (BDMA) was transformed into the final benzylidene cyanoacetate (BCA) with a 99% yield at 80 °C and solvent-free conditions. Compared to the random NENU-5+CuCo-LDH, the NENU-5@CuCo-LDH with spatially separated acid-base sites indicated a higher reaction rate due to the designed reaction sequence and the shorter mass transfer pathway. Moreover, this hierarchical structure showed inherent shape selectivity and extraordinary stability. This study introduces spatial separation to address the incompatibility issue between inorganic acid and base active sites, offering novel perspectives for acid-base systems.