Although nanozyme-based colorimetric assays have been broadly used for biosensing, some limitations such as low catalytic activity of nanozyme, poor sensitivity to analytes and lack of understanding the structure-activity relationship remain unsolved. In this work, we developed an ultrasensitive colorimetric method for biothiols detection based on density functional theory-assisted design of janus Pd–Fe3O4 nanozyme. The Pd–Fe3O4 dumbbell-like nanoparticles (DBNPs) prepared by seed-mediated approach shows a uniform heterodimeric nanostructure. Ultrasensitive biothiols detection is achieved from two aspects. On one hand, due to the synergistic effect between Pd and Fe3O4 in the dumbbell structure, Pd–Fe3O4 DBNPs show enhanced peroxidase-mimic activity compared to the individual components. On the other hand, when the target biothiols molecule is present, its inhibition effect on the janus Pd–Fe3O4 nanozyme is also significantly enhanced. The above results are confirmed both in experiment and theoretical calculation. Based on the rational design, a simple, highly selective and urtrasensitive colorimetric and quantitative assay for biothiols is developed. The limit of detection (LOD) can reach as low as 3.1 nM in aqueous solution. This assay is also successfully applied to the detection of biothiols in real urine samples. Moreover, the Pd–Fe3O4 nanozyme is used to discriminate biothiols levels in normal and cancer cells with high sensitivity at the cell density of 15,000/mL, which demonstrates its great potential in biological and clinical analysis. This work not only shows the great promise of janus bimetallic nanozymes’ excellent functionalities but also provides rational guidelines to design high-performance nanozymes for biosensing and biomedical applications.