In this study, we utilized typical Chinese medicine herbal residues (CMHRs)-Scutellaria baicalensis (Scutellaria baicalensis Georgi) residue (SR), as the raw material and employed Na2SiO3 and Fe2(SO4)3 as modifying agents to fabricate a novel and multifunctional hydrochar (FeSi-SRHC), which was designed for comprehensive removal of typical contaminants such as Cu2+, Zn2+, tetracycline (TC), and ciprofloxacin (CIP), along with relevant bio-contaminants (resistant bacteria (RBs) and resistance genes (RGs)) present in wastewater. Based on the analysis of adsorption kinetics and Freundlich isotherm, it was found that FeSi-SRHC exhibited physical monolayer adsorption for Cu2+/Zn2+ while mainly chemical multilayer adsorption for TC/CIP in single-contamination system. Furthermore, Langmuir isotherm demonstrated excellent adsorption capacity of FeSi-SRHC towards Cu2+/Zn2+/TC/CIP with maximum capacities of 255.75, 265.26, 425.53, and 404.86 mg/g, respectively. In the co-contamination system, the presence of Cu2+, Zn2+, TC, and CIP exhibited varying degrees of inhibitory or promotive effects on the mutual adsorption by FeSi-SRHC. This divergence stemmed from differences in complexation intensities and concentration ratios among diverse co-existing contaminants. Based on XPS and Density Functional Theory (DFT) analyses, the adsorption process for Cu2+, Zn2+, TC, and CIP by FeSi-SRHC primarily involves pore fill, complexation reactions, ion exchange, hydrogen bonding, π-π stacking interactions, and electrostatic interactions. Bio-contaminant removal experiments revealed that the release of baicalin and wogonoside from FeSi-SRHC disrupts the structure of RBs cells and compromises the integrity of resistance plasmids. The practical application experiment showed that FeSi-SRHC displayed favorable performance for removing heavy metals, antibiotics, and bio-contaminants in actual wastewater. This study presented a “Treating waste with waste” strategy, which provided a method with low carbon, eco-friendly, and inexpensive for CMHRs resources and turning waste into treasure while proposing a idea to address the challenges associated with treating heavy metal, antibiotic, and bio-contaminant contamination in wastewater.