The invention relates to a high throughput test method for a tomato bacterial disease, and more particularly relates to a high throughput test method which can utilize a locking probe to carry out reverse dot blot hybridization on tomato bacterial wilt original bacteria, tomato ulcer pathogenic bacteria and a tomato spot disease, and belongs to the crop preventing and curing disease and exit and entry plant quarantine range. The high throughput test method provided by the invention is based on a rolling circle amplification technology of the locking probe, a pair of universal primers are utilized for amplifying multiple pathogens, then, the high throughput test method and a reverse dot blot are combined together, a result is judged through a chromogenic reaction, the testing time of the traditional tomato bacterial disease is shortened, the specificity and the sensitivity of the detection are guaranteed, and the high throughput test is realized. According to the method, the testing cycle of the traditional pathogenic bacteria can be shortened, the cargo clearance can be increased, the intercept and capture relevance ratio of epidemic situations of imported bulk farm-product is improved, the pest invasion capacity is improved, the cargo clearance of cargoes imported and exported at ports in China is accelerated, and the enterprise cost is reduced and the high throughput test method has the important meanings.