Encapsulating natural enzymes in metal–organic frameworks (MOFs) can maintain the original biological functions of enzymes in harsh environments. However, the nature of interfacial interactions between a MOF and enzyme is currently unclear, rendering effective regulation of the biocatalytic activity of the enzyme@MOF composite difficult. Differences in the hydrophilicity of MOF carriers are closely related to the conformational changes and catalytic properties of the enzyme. In this study, the catalytic activity, stability, and conformational changes of alkaline phosphatase (ALP) encapsulated in hydrophilic zeolite imidazolate framework-90 (ZIF-90) and hydrophobic ZIF-8 were systematically investigated using experimental methods and molecular dynamics simulations. The results demonstrated that hydrophilic ZIF-90-encapsulated ALP exhibited superior stability and was 2.22-fold more retained catalytically active than hydrophobic ALP@ZIF-8 after 20 cycles of utilization. Moreover, the hydrophilic interface provided by ZIF-90 effectively regulated the structure of ALP to maintain the optimal catalytic conformation of its active center. The practical application of highly bioactive ALP@ZIF-90 was demonstrated by employing it in a self-calibrated colorimetric/fluorescence dual-mode sensing method for the efficient, reliable, and accurate detection of methyl paraoxon. This study provides new insights for improving enzyme immobilization strategies and promoting the rapid development of enzyme@MOF composites for catalytic and sensing applications.