In order to explore the effects of tillage methods, organic fertilizer replacing part of chemical fertilizer and straw returning on Fusarium head blight and crown rot, the field experiments were carried out from 2022 to 2024. The two factors of tillage methods and organic fertilizer replacing part of chemical fertilizer were designed by split-plot design. The tillage methods were set as DT (tillage every other year, tillage depth of 25 cm) and RT (rotary tillage in successive years, tillage depth of 15 cm) in the main area, and the organic fertilizer replacing part of chemical fertilizer was set as OMC (fermented cow manure organic fertilizer replacing 25% basal fertilizer), OMP (fermented pig manure organic fertilizer replacing 25% basal fertilizer) and CK (conventional fertilization) in the sub-area. The factors of straw returning were designed by large area comparison. The results showed that there was no significant difference in the ear rate of scab between deep tillage and rotary tillage in a maize-wheat rotation cycle after years of monoculture of cotton. Under deep tillage, the application of fermented cow manure organic fertilizer could significantly reduce the disease spike rate of wheat scab, and the control effect of disease spike rate was 6.4%, while the effect of fermented pig manure organic fertilizer was not significant. Under rotary tillage, the application of fermented cow manure and pig manure organic fertilizer had no significant effect on reducing the spike rate of wheat scab. Under the condition of no straw returning, there was no significant difference in the disease spike rate of fermented cow manure or pig manure organic fertilizer, but there was an increasing trend. The ear rate of wheat scab in maize straw returning treatment was significantly lower than that in non-returning treatment, and the control effect of ear rate was 34.2%. Under the same genetic background, the increase of yield and the decrease of scab ear rate caused by environmental factors are a pair of contradictions. Based on two maize-wheat rotation cycles after multi-year monoculture of cotton, under conventional fertilization, rotary tillage in the next year of deep tillage can significantly reduce the incidence of stem base rot compared with continuous rotary tillage, and the disease index control effect is 9.0%. Under deep tillage, the application of fermented cow manure organic fertilizer could significantly reduce the incidence of stem base rot compared with conventional fertilization, and the disease index control effect was 34.2%, while the application of fermented pig manure organic fertilizer was not significant. Under rotary tillage, the application of fermented cow manure organic fertilizer could significantly reduce the incidence of stem rot, and the disease index control effect was 23.4%, while the application of fermented pig manure organic fertilizer increased significantly. The incidence and disease index of wheat stalk rot were significantly lower in the maize straw returning treatment than in the non-returning treatment, and the disease index control effect was 11.0%.