The invention provides a microbial agent for preventing and treating cumquat huanglongbing and a preparation method thereof, and particularly provides a microbial agent for preventing huanglongbing of cumquat, citrus shantianju and citrus and a preparation method thereof. The microbial agent is formed by fermenting and then mixing bacteria like Gulake streptomyces, Kawuer streptomyces, bacillus psychrosaccharolyticus, nissl bacillus and tufted trichoderma proportionally. Procreation and propagation of gram negative bacteria are inhibited by means of root irrigation and foliage spray, bacteria are used to treat bacteria, and harmful pathogenic bacteria in soil are killed, so that tree root systems are more developed, tree cell tubes are smooth, yellow leaves of fruit trees are turned green, and healthy new treetops are enabled to grow; the microbial agent generates insecticidal antibiotics like flavensomycin and inhibits or damages development process of eubactericera and eggs of other disease-transmitting insect (like citrus aphid), so that adult rate is reduced, orchard pest occurrence quantity is reduced, transmission media of huanglongbing are cut off, and effects on preventing and controlling citrus huanglongbing are realized.