The accurate quantitative detection of trace antibiotics in the complex biological sample is of great significance for the investigation of drug residues and metabolism. A graphene oxide-modified chitosan hydrogel (GO-CMCS) was meticulously fabricated and explored the antibiotic residues and metabolic regularity of antibiotics (enrofloxacin and tetracycline) in mice using a solid-phase extraction (SPE) technique in conjunction with ultra-high-performance liquid chromatography (UHPLC). The GO-CMCS hydrogel was prepared by GO incorporate into CMCS hydrogel via Schiff base reaction displaying a plated structure with voids primarily composed of microporous and mesoporous structure, facilitating the adsorption of trace amounts of antibiotics. Under the optimized conditions, GO-CMCS-based SPE-UHPLC method affords the low limits (0.26–0.74 ng/mL), satisfactory spiked assay recoveries (83.10–88.00%) with all relative standard deviation values less than 6.74%. Then the adsorption mechanisms of antibiotics were investigated by utilizing the isothermal adsorption model, kinetic model, and intra-particle diffusion model. After intravenous administration of two antibiotics, mice in vivo exhibited different drug metabolism regularity, the concentration of tetracycline increased from 0.457 to 0.663 μg/mL before 30 min and then continuously decreased, but the concentration of enrofloxacin quickly dropped from 1.643 to 0.061 μg/mL during from 10 to 150 min. The antibiotic residues and metabolic regularity in mice were successfully detected by established method.