The present invention relates to a deodorizing apparatus using native microorganisms. Specifically, the present invention relates to a deodorizing apparatus using native microorganisms for removal of malodors of sewage treatment plant sludge, comprising a native microorganism activating tank, where a colony of the native microorganisms in a spore state is germinated and activated through a proliferation process under conditions where oxygen and organic materials are supplied, and the native microorganisms returned from a second deodorizing tank is further activated; and a first and a second deodorizing tanks which remove malodorants from untreated matter under conditions where oxygen and the activated native microorganisms are continuously supplied. The deodorizing apparatus of the present invention, which is an eco-friendly and economical method using native microorganisms, can effectively remove malodor generated from various types of sludge including a primary sludge, a secondary sludge, a sludge containing night soil, etc. produced from sewage treatment plants.