The invention is a method for fast identifying host proteins interacting with pathogenic germs, relating to a method of applying Gram positive and negative unactivated pathogenic germs to fast separate and purify host proteins interacting with them, providing a method for fast and reliably detecting and identifying host proteins interacting with pathogenic germs, comprising: using formaldehyde tounactivate pathogenic germs; using eluent to remove easy-to-drop components on outer membranes of the pathogenic germs; letting the pathogenic germs and host proteins hatch, and letting host proteinswhich can interact with the pathogenic germs adhere to surfaces of the pathogenic germs; collecting the host proteins interacting with the pathogenic germs by eluent. And the invention can avoid the problem that the host proteins interacting with activated germs are polluted by outer membranes of the pathogenic germs or secrete proteins. And all the obtained proteins derive from the host, having no pathogenic germ pollutants, and it is a method for in high efficiency and reliably detecting composition of proteins in host taking part in first line of defence in pathogenic germ defending system.