The invention relates to a system for detecting multiple quantitative and virulent genes of H.pylori as well as kits and applications of the system. The system for detecting multiple quantitative and virulent genes of H.pylori comprises multiple pairs of primers, each for strain identification genes (16S rRNA), quantitative analysis genes ureCand Beta-globin, as well as virulent genes (cagA, vacA-s1, vacA-s2, vacA-m1, vacA-m2, iceA1, iceA2, dupA, oipA and luxS). The system for detecting multiple quantitative and virulent genes of H.pylori and the kits of the system can directly perform synchronous detection and analysis on the strain identification, quantification and virulence of a tissue sample in a same reaction system without adopting a conventional culture step or other steps, remedy defects that a conventional detection method is low in throughput, time-consuming and low in detection rate, obviously improve the accuracy of detection results, immediately provide a comprehensive, accurate and low-cost etiological diagnosis for clinic, and provide an important reference for the accurate diagnosis, differential diagnosis and disease prognosis of H.pylori infection.