The promotion of portable antibiotic rapid detection technology and instruments is of critical importance across various fields, including food safety, environmental monitoring, and healthcare. Building on the kanamycin aptamer electrochemical sensing platform and auxiliary test instruments developed in previous research, this study successfully overcomes the limitations of traditional electrochemical workstation by introducing a portable multi-channel electrochemical analyzer. This innovative device requires only the appropriate biosensor chip to detect relevant targets. It has been effectively utilized for both end-point and real-time detection of kanamycin and tetracycline in water samples. End-point quantitative analysis conducted at 20 minutes revealed detection limits of 0.49 and 45.1 μmol/L for kanamycin and tetracycline, respectively. The real-time analysis demonstrates the capability to differentiate between varying concentrations of kanamycin samples at an early stage. The sensor chip construction method is straightforward and exhibits good selectivity for the relevant targets, enabling rapid detection of different antibiotic residues in actual water samples. Furthermore, the portability of the self-developed electrochemical analyzer is anticipated to accelerate the practical implementation of antibiotic residue detection.