In order to identify characteristics, genesis and reservoir significance of vesicle filling, volcanic rocks with amygdules of Carboniferous Batamayineishan Formation were sampled in eastern Junggar Basin. Based on thin section observation, EPMA, geologic thermometer and vesicle filling rate analysis, the amygdules were characterized. The results show that the filling minerals include silica, zeolite, celedonite, chlorite, and saponite. There are two filling models, mono- and multiple component ones. Mono-component amygdules include silica and celedonite ones. 10 types of multiple component amygdules can be recognized, including quartz→zeolite, chlorite→quartz, and quartz→celedonite→saponite. The formation temperature of chlorite at the edge of amygdales is between 84.7 and 123.6 ℃,which indicates a low temperature filling process. The amygdules form from precipitation and crystallization of epigenetic fluid. The quality of volcanic reservoirs becomes worse due to the vesicle filling process. 94.5％ of the primary vesicle space is completely lost. Although vesicle filling has such a negative influence on reservoir quality, residual amygdule inner pores and amygdule shrink pores still have some reservoir capability. In addition, the dissolution pores generated by the fluid which participate in the formation of amygdule can also compensate the reduction of vesicle volume to a certain extent.