The straw incorporation in paddy fields exacerbates the reductive toxicity caused by flooding during the rice tillering stage in cold regions. Mid‐drainage can alleviate reductive toxicity, while nitrogen fertilizer (NF) application can enhance the drought resistance of rice. However, there is still a lack of convincing evidence about the types of reductive toxicity and appropriate draining thresholds with straw incorporation. A field experiment was conducted in northeast China to investigate the reductive toxicity of paddy fields caused by flooding and straw incorporation. Primarily, the study aimed to investigate the reduction of toxicity caused by straw incorporation. Additionally, the investigation verified the role of varying NF (0, 50, 100, 150 kg N ha−1) in conjunction with mid‐season drainage (−15 cm) to mitigate soil reductive toxicity while preserving root activity. Before mid‐season drainage, the contents of soil total amount of reductive matter, active reductive matter, Fe2+, and Mn2+ were 5.1–5.9 cmol kg−1, 3.2–3.9 cmol kg−1, 399.4–410.1 mg kg−1 and 290.3–340.1 mg kg−1, respectively. Mid‐season drainage of 15 cm depth decreased the total amount of reductive matter, active reductive matter and Fe2+ content by 51.8%, 56.0% and 29.6%, respectively. However, upon rewetting, the content of reductive substances reverted to pre‐drainage levels. Drainage led to a reduction in soil organic acid content by 56.6–78.8% and an increase in rice root activity by 160–290%. While increased NF application correlated with higher rice root activity, a significant yield increase was only observed within the range of 0–100 kg ha−1. In summary, an alternate wetting and drying threshold of −15 cm in combination with 100 kg ha−1 of NF rate significantly increased root activity and reduced reductive toxicity of the tillage layer without decreased rice yield. The reductive substance content rebounded to the pre‐drainage level after reflooding in the subsequent growth stage. Therefore, to minimize the reductive toxicity and methane emission caused by straw incorporation, rice fields can be drained to a depth of 15 cm during mid‐season drainage. Additionally, the fields should be drained several times in the following growth stage.