The invention provides a device and process for advanced treatment of immobilized functional microbe wastewater and belongs to the technical field of sewage treatment. The treatment device comprises an intermediate regulating tank, a facultatively anaerobic BAFB reactor, an aerobiotic BAFB reactor and a sedimentation tank which are connected in sequence. The treatment process comprises the steps that 1, physical-chemical treatment is performed; 2, a facultatively anaerobic BAFB process is performed; 3, an aerobiotic BAFB process is performed; 4, a sedimentation and reflux process is performed; 5, mud-water separation is achieved through the sedimentation tank, and discharged water reaching the standard is discharged. The existing problems of low substrate concentration, microbial biomass limitation, biotoxin inhibited microbe growth and the like of secondarily treated discharged water can be well solved. In addition, the device and the process for advanced treatment of immobilized functional microbe wastewater have the advantages of being good in pollutant removal effect, simple in treatment process, convenient to operate and manage, small in occupied area, low in infrastructure investment, free of peculiar smell and stable in discharged water quality and meets the discharge requirements.