Antibiotic residues in the environment and in foods pose a serious threat to ecosystems and human health. Developing sensitive and on-site detection methods is therefore in high demand. In this work, a portable paper-based colorimetric sensor with a smartphone platform with an ultrahigh sensitivity has been designed for on-site and quantitative analysis of antibiotic residues based on aptamer-regulated nanozyme activity. The developed excellent peroxidase-like nanozymes, carbon-protected NiCo bimetal oxides with a unique hollow nanocage structure (NiCo@C HCs), could effectively catalyze the oxidation of chromogenic substrates by H2O2. Once bound to a specific aptamer, the enzyme-mimicking activity of NiCo@C HCs is obviously inhibited as a result of the masking of active sites but could be restored via the target-aptamer recognition. Herein, the aptamer-modified NiCo@C HCs are embedded on paper pieces to construct paper-based biochips for visual detection. Meanwhile, a smartphone platform is integrated for the signal readout. Using enrofloxacin (ENR) as an analyte model, the proposed paper-based analysis platform shows a reliable and sensitive detection of ENR with an ultralow detection limit of 0.029 ng/mL. The platform also works well in various real samples. This analysis method is facile in design, showing a great application potential for on-site and mass screening of antibiotic residues in the environment and in foods.