In the present study, attapulgite (AT), biochar (BC) and zeolite (ZO) were utilised as three distinct categories of exogenous porous passivators (EPP) in the construction of the anaerobic digestion system for chicken manure. The present study set out to analyse the morphological changes of organic nitrogen, organic phosphorus and copper (Cu), zinc (Zn) and heavy metal ions (HMs) in the digestion system by means of colourimetry and the BCR continuous extraction method. Furthermore, the passivation mechanism of Cu, Zn and the transformation and removal mechanism of nitrogen and phosphorus in the digestion system were explored by Infrared Spectroscopy (IR), X-ray diffraction (XRD) and three-dimensional fluorescence spectrum (EEM) characterization. The findings demonstrated that the incorporation of EPP could mitigate acid inhibition in the anaerobic digestion process. The addition of AT and ZO exhibited the most significant impact on the adsorption and transformation of total nitrogen (TN) and total ammonia nitrogen (TAN), which increased by 30.43% and 26.30% compared with the control group; The addition of ZO and AT had the most significant impact on total phosphorus (TP) and total phosphate (TPS), which increased by 9.33% and 17.74% compared with the control group; The contents of extractable (WA) and reducible (RD) copper and zinc in the three EPP groups were lower than those in the control group. The concentrations of WA and RD of Cu and Zn in the AT group were found to be 15.97% and 6.18% lower than those in the control group.