Abstract: Manure can often contain various veterinary drug residues and a large amount of dissolved organic matter (DOM). These veterinary drug residues can enter the soil after manure application, and then enter the water bodies through runoff and leaching, thereby posing a potential risk to ecosystem safety and human health. Moreover, the DOM can dominate the transport of the veterinary drug residues in soil. However, both experimental and modeling are still lacking in exploring the impact of the manure DOM and its components on the transport of the veterinary drug residues in soil. Particularly, Phyllostachys praecox plantations have been widely distributed in southern China. A large amount of the manure has been applied during cultivation. Therefore, this study focused on the antibiotic transport in the soil of the intensively managed Phyllostachys praecox plantation. Transport experiments were carried out in the repacked columns (5 cm in diameter and 10 cm in height) of the soil aggregates under saturated conditions. A systematic investigation was then made to explore the effects of the pig manure DOM and its hydrophilic (HI) and hydrophobic (HO) fractions on the transport of the veterinary drugs (doxycycline, sulfamethazine, enrofloxacin, and florfenicol). In all inflow treatments, the sulfamethazine and florfenicol exhibited the high recovery rates (≥58.4% and ≥60.9%, respectively) in the outflows from soil columns. While no enrofloxacin and doxycycline were detected in all outflow samples. Both sulfamethazine and florfenicol also shared the higher potential to leach into the shallow groundwater after rainfall and irrigation. The pig manure DOM and its HO fraction increased the recovery rate of florfenicol (by more than 20%). The water-soluble complexes were formed after additions. Contrastingly, the HI fraction of the pig manure DOM slightly reduced the recovery rate of the florfenicol. It was possible to bind with the florfenicol via the hydrogen bonding and subsequent co-adsorption onto the soil particles. As such, the pig manure DOM dominated the transport of the sulfamethazine. Only the additions of its HI and HO fractions at the high concentration (100 mg/L) then led to a slight (by less than 10%) increase and decrease in the recovery rate of the sulfamethazine, respectively. The performance of the two-region model (TRM) (R²: 0.966−0.993; root mean square error: 0.019−0.039) was better than that of the convection dispersion (R²: 0.951−0.992; root mean square error: 0.022−0.046) after simulation on the breakthrough data of Br^-. The better performance of the TRM was achieved in the macropores for the water transport in the repacked columns of the soil aggregates. The TRM also performed better to simulate the non-equilibrium transport of the veterinary antibiotics (R²: 0.908−0.997; root mean square error: 0.014−0.092). Differences in the calibrated model parameters between inflow treatments showed that the DOM and its polarity fractions dominated the transport of the veterinary antibiotics via the adsorption site fraction in the mobile water region and inter-regional mass transfer coefficient. Strongly sorbing veterinary drugs doxycycline and enrofloxacin failed to pass through the soil column under all inflow treatments. There were different mechanisms of the manure-derived DOM and its polarity fractions on the veterinary drug transport. The finding can provide a scientific basis to optimize the selection of the manure products into the Phyllostachys praecox plantations, in order to minimize the risk of antibiotic pollution on the local water bodies.