Objective To analyze the drug resistant characteristics of 84 clinical isolated Helicobacter pylori (Hp) strains, and to observe the inhibitory effects of anti-Hp Lactobacillus acidophilus (La)4 and La6 on different antibiotic-resistant Hp strains. Methods Hp strains were isolated and cultured from gastric mucosa of 84 different gastropathy patients (20 patients with chronic gastritis, 24 with gastric ulcer, 19 with duodenal ulcer and 16 with gastric cancer). The minimum inhibitory concentration (MIC) of metronidazole, clarithromycin and amoxicillin were tested by E-test in order to determine the resistance of these three antibiotics in clinical isolated Hp strains. With standard La as control, the supernatant of anti-Hp La4 and La6 was added into Hp strains culture wells. Hp strains were cultured in solid media for 72 hours, and then inhibition ring were recorded. Anti-Hp Lactobacillus acidophilus liquid was also added to culture medium of different Hp strains, which were in liquid culture, culture medium were taken at different time points (4,8,12,24,48 hrs) to calculate bacteria colony number and test urease activity. Results In 84 clinical isolated Hp strains, the resistant rates of metronidazole, clarithromycin and amoxicillin resistance rates were 67.9%, 17.9% and 1.2% respectively. Of those 11 strains were mixed drug resistance, which included 10 strains of metronidazole and clarithromycin mixed drug resistance, and one of metronidazole and amoxicillin mixed drug resistance. In solid culture conditions, supernatant of anti-Hp Lactobacillus acidophilus La4 and La6 had obvious inhibitory effect on antibiotic-resistant and non-resistant Hp strains. In liquid culture conditions, anti-Hp Lactobacillu acidophilus La4 and La6 bacterium liquid could inhibit the proliferation of antibiotic-resistant and non-resistant Hp strains, the antagonistic role was significantly stronger than the standard Lactobacillus acidophilus strains (P<0.05). The urease activity of antibiotic-resistant Hp strains was inhibited since mixed cultured with anti-Hp Lactobacillu acidophilus La4 and La6 for 4 hours, the urease activity gradually decreased as culture time extended, and the inhibitory role was significantly stronger than the standard Lactobacillus acidophilus strains (P<0.05). Conclusions In 84 Hp strains, most were metronidazole resistant strains, followed by clarithromycin resistant strains, metronidazole and clarithromycin mixed resistance strains. In vitro, anti-Hp Lactobacillu acidophilus La4 and La6 had obvious inhibitory effects on antibiotic-resistant and non-resistant Hp strains.