Disclosed is a pharmaceutical composition for inhibiting infection and replication of influenza A and B virus, and the manufacture thereof. The pharmaceutical composition is produced by a manufacture of low-temperature disintegrating cyanobacteria, comprising the steps of: (a) mixing cyanobacteria and non-organic solvent to form a suspension containing cyanobacteria; (b) freezing the suspension with a temperature below 0° C. to form a ice block and the ice block being melted at a low temperature, the whole step being repeated at least twice; (c) separating the cyanobacterial residues and extract solution of the suspension; and (d) collecting the isolated cyanobacterial extract solution; wherein the cyanobacterial extract solution is a solution containing cyanobacterial bioactive substances. The pharmaceutical composition is able to effectively inhibit binding of sialic acid and hemagglutinin of influenza A and/or B virus, so as to inhibit infection and replication of influenza virus. Further, this pharmaceutical composition is able to inhibit infection of influenza virus resistant to neuraminidase inhibitors.