Anaerobic digestion (AD) is a key technology for the utilization of livestock and poultry excrement, but the complex pollution of heavy metals and antibiotics in manure is catching more attentions. In this study, AD of swine manure loading with four types of biochar produced and characterized in our lab was performed, in which the effects of biochar on the stability of AD and the methane yields were focused, and the removal of antibiotics and migration of heavy metals were investigated as well. The results showed that the removal efficiencies of sulfadimidine and tylosin were remarkable in AD. In particular, the removal rate of tylosin was higher than 99.90%. But the biochar didn`t show credits in the antibiotics removal. The maximum methane yield of 146.98 mL/ (g VS) was noted in the digester added with the biochar derived from paper mill sludge (BPMS) which was distinguishing for containing 87.35% of ash, with a high pHPZC of 8.95, and having more mesopores and macropores. In this reactor, 12.40% of Cu was moved to the solid phase via BMPS adsorption, and 70.26% of Zn and 82.80% of As in the liquid were migrated to the solid digestate. Moreover, compared to the heavy metal speciations in the digestate from the control digester, the content of the acid soluble Cu in the digester loaded with BMPS was decreased to 7.99%, and no acid soluble Zn was found along with a drop of 29.20% for the reducible Zn, and the content of the residual As was increased by 16.60%. It revealed that BPMS had a great potentiality to remove As and Zn in wastewater and synchronously mitigate the bioavailability of Cu/Zn/As in the digestate. Herein, applying BPMS in the AD of swine manure could reduce the complex pollution of heavy metals and antibiotics, and obtain a higher methane yield simultaneously.