With the rapid development of socialization and industrialization, more and more pollutes were produced and discharged into natural environment. It is harmful to human health and life. These pollutes included refractory degradation organic compounds like PAHs, RDX, HMX, CL-20, PCBs and alkanes and their relative substances. Various compounds exist in nature with long life span. They are the most hazardous than other organics. The impact of pollutes can be treated by microorganisms. Result showed that it is an effective way for bioremediation of these pollutes with microbial metabolism or cometabolism. A few key enzymes, mainly oxidative and reductive enzymes, connected with the first step of initial degradation. Normally, enzymes grouped with other active fraction on the cell membrane are composed of one oxidative and reductive system for substrates oxidation. The metabolic intermediates can be used with TCA by microorganisms. The pathways of metabolism and the key enzymes were summarized. The further research topics should be focused on microorganism screen and its relative enzyme, pathway and mechanism of metabolism or cometabolism for such compounds degradation, and the result was hoped for the environmental protection.