Disclosed are a method for diagnosing thalassemia based on a liquid chip system, and a kit and an application. The present invention designs probes for detecting a, ß thalassemia genetic defect types. These probes are respectively cross-linked and mixed with fluorescent encoding microspheres of different colors to obtain liquid chips for diagnosing a, ß thalassemia. After PCR amplification is performed, by using a specific primer of the present invention, on a sample to be detected, a biotin-labeled PCR product is obtained, which is then hybridized with the liquid chip of the present invention, and further undergoes fluorescence labeling by use of phycoerythrin. Finally, a detection result is read out through a liquid chip detector. The kit of the present invention comprises PCR primers and specific probes, and can detect deletion or non-deletion point mutation a, ß thalassemia.