The effects of different tillage practices on soil organic carbon (SOC), soil aggregation, soil fulvic acid (C‐FAF), soil humic acid (C‐HAF), and soil humin (C‐HUM) contents at 0–5, 5–10, and 10–20 cm layers under double‐cropping rice (Oryza sativa L.) fields in southern China were explored. The experiment included four tillage treatments: conventional tillage and crop residues incorporation (CT), rotary tillage and crop residues incorporation (RT), no‐tillage and crop residues incorporation (NT), and rotary tillage without crop residues as a control (RTO). The results showed that SOC content under RT and CT treatments were significantly higher than that of RTO treatment. The percentage of soil aggregates of <0.001 mm, 0.005–0.001 mm, and 0.01–0.005 mm at 0–5, 5–10, and 10–20 cm layers under CT treatment were significantly higher than that of RTO treatment. The C‐HUM, C‐FAF, and C‐HAF contents were increased by combined application of tillage with crop residues practices. The results showed that C‐HUM, C‐FAF, and C‐HAF contents under CT and RT treatments were significantly higher than those under the RTO treatment at 0–5, 5–10, and 10–20 cm layers. As a result, it is an appropriate soil practice for increasing SOC content, soil aggregation, and humic substances under double‐cropping rice fields in southern China under conventional tillage and rotary tillage.