In order to select the best method to remove microorganism of Pyropia haitanensis, we treated P. haitanensis thallus with different combinations of ampicillin, gentamicin sulfate and kanamycin. Meanwhile, we explored the relationship between the growth of P. haitanensis thallus and the change of microflora. The results showed that low concentration of gentamicin sulfate (10 μg/mL) or high concentration of kanamycin (800 μg/mL) could inhibit the growth of P. haitanensis thallus. In contrast, ampicillin of each concentration in this paper had a promoting effect on the growth of P. haitanensis thallus. We chose the combination of ampicillin (500 μg/mL), gentamicin sulfate (500 μg/mL) and kanamycin (300 μg/mL) treating P. haitanensis thallus for 24 hours. The combination of antibiotics could obviously inhibit the microbes and had no side effects on the growth of Pyropia. The discs in different strains of P.haitanensis, different-day-old and culture density of P. haitanensis, different salinity and concentration of medium were all growing faster in antibiotics treated groups than control group. Moreover, two special bacteria strains, whose morphology of colonies and strains were different between antibiotics treated groups and control group, were found after comparing bacteria strains isolated from antibiotic treated groups and control group. Based on the above results, a certain type of microorganism multiply rapidly which inhibit growth of the other microorganism that were benefited for the growth of P. haitanensis thallus. When the microorganism that inhibit growth were inhibited with antibiotics, the probiotics became the advantage group and promoted the growth of blades. The probiotics was not sensitive to antibiotics, but with the change of culture condition, the effect of antibiotics on the strains that inhibited the growth of Pyropia became weaker, thus they multiplied rapidly, as a result, hindering the growth of Pyropia thallus.