The objective of this study was to investigate the temporal and spatial distribution of antibiotics in agricultural soils of Huang-Huai-Hai Plain, which is a major agricultural producing area and economically developed region in China. In this study, 105 soil samples including 13 groups of soil profile samples (0–20, 20–40 and 40–60 cm) and 23 paired surface soil samples of greenhouse and open-field were collected from four provinces/municipality in 2018. The occurrence of 20 antibiotics, including four tetracyclines (TCs), seven quinolones (QNs), six sulfonamides (SAs) and three macrolides (MLs) were measured. The concentrations of total antibiotics fell in the range of 1.62–575 μg kg−1, with the mean value of 68.8 μg kg−1. TCs and QNs were dominant antibiotics in soil, accounting for 99.6% of the total concentration. Regional differences of antibiotic residues in soil were found among the four regions as well as between different cropping systems. The levels of antibiotics in greenhouse soils (3.52–575 μg kg−1) were higher than those in open-field soils (1.62–142 μg kg−1). In soils of greenhouse of 1–6 years old, the levels of antibiotics were higher than those with longer history (7–30 years). Antibiotics were mainly distributed in the depth of 0–20 cm. The total concentrations of antibiotics/QNs followed the order of 0–20 cm > 40–60 cm > 20–40 cm, due to probably their interactions with total organic carbon and associated bacterial communities. The results in the study will provide data supports for the formulation of soil antibiotic contamination prevention and control measures.