Molecular interaction detection is a hot topic in the fields of food safety detection, clinical cancer pathological screening, and other areas of research. To realize real-time and rapid detection of interactions between biomolecules, a molecular interaction detection system based on a fiber biosensor was designed in this study. The coupling structure of a self-focusing lens and quartz fiber was adopted to improve the coupling efficiency of optical transmission between the light source and interference light. A STM32 microprocessor was used as the main controller to realize data acquisition, 3D transmission mechanism control, constant temperature oscillation control, and other functions. Finally, the designed and BLItz molecular interaction detection systems were used to detect the different concentrations of immunoglobulin IgG and protein A, respectively. The binding and dissociation reactions of the IgG molecule and antigen molecule protein A were detected in real time. The experimental results show that the detection limit of the system could reach 10 μg/mL, and the repeatability CV value was less than 6%, which was close to that of the BLItz. The designed system has the advantages of high automation, no need for cleaning, no cross contamination in the detection process, and low cost. Therefore, it can meet the needs of pharmacokinetics research.