GAC will be effective for the advanced treatment in drinking water due to the aggravating micro-pollution of drinking water source in China, but the chemical security of GAC filter effluent should be taken into account. It was proved that the micro-organic matter in the GAC filter effluent still was in a higher level of quantity, such as AOC density (211 μg/L). And some new organic matter was tested in the effluent. The effects of carbon characters, source water quality and operation of AC process on the removal results of micro-organic matter were investigated. The GAC process removed effectively the disinfection by-products, while not steadily sometimes. The BAC process also removed the HAAs precursor; but it was limited to remove the THMs precursor. The adsorptive ability of AC to remove disinfection by-products was limited, depending on the characters of AC and the one in drinking water. AC could remove the majority of ozonation by-products including inorganic by-products (formaldehyde) and organic by-products (bromate). However, when the plant used purify oxygen to produce ozone, the removal effect was different from bench scale. And BAC was used for removal of microcystins (MC), which was influenced by source water quality. Most part of MC was degraded by microorganism, other part of MC was adsorbed by AC. In addition, AC removed the Ames mutagens effectively to ensure the safety of drinking water, even if AC adsorbed the total organic carbon to the maximum.