The invention discloses an oligonucleotide chip labeling a random primer PCR amplification based on a biotin-avidin-cy3 reaction system, which is made by a substrate, and CMV, HSVI, RV, EBV or TB pathogen probes, a negative control, a positive control and a blank control that are coated on the substrate in an array way, wherein the substrate is a surface aldehyde glass slide; the pathogen probes are 10 of CMV-1, CMV-2, HSVI-1, HSVI-2, RV1, RV2, EBV1, EBV2, TB1 and TB2 probes with 70mer; the positive control is a synthesized marker probe; and the blank control is double distilled water. The invention performs the biotin-11-dUTP amplified labeling to various pathogen target sequences by using the random primer and detects the pathogen by adopting a method of increasing the labeling efficiency through using a biotin-avidin-cy3 signal amplification system, has high detection sensitivity and obviously shortens the detection cost and the detection time. The technical system can be suitable to the fields of clinical detection, health supervision, customs quarantine control, scientific research, and the like.