Purpose <p>Fertilization, a widely used agricultural management practice to maximum crop yields, significantly influences microbial community structure and diversity. Soil microbial communities are known to differ across plant growth stages, but how different organic and inorganic fertilization regimes shape microbial temporal variation remains unclear.</p> Methods <p>To investigate the temporal stability of microbial communities under organic and chemical fertilization, rhizosphere soil of sorghum was collected at four growth stages (jointing, heading, filling and maturity) in a long-term field experiment with multiple chemical and organic fertilization treatments.</p> Results <p>The results showed that, compared with the control and chemical fertilizer treatments, organic manure treatments resulted in less pronounced variation in microbial community diversity and structure across growth stages. Microbial cooccurrence networks in organic manure treatments were more robust compared to the control and chemical fertilizer treatments, indicating greater stability of microbial community temporal variation in organically fertilized soils. Across different growth stages, fungal communities in manure treatments showed no significant differences in diversity or community structure, and maintained low average variation degree, whereas bacterial communities were more variable.</p> Conclusion <p>These findings suggest that microbes in organically fertilized soils have more stable communities over time, with fungal communities being more stable than bacterial ones. This study provides insights into how fertilization shapes microbial communities and indicates that organic fertilization enhances the resistance of microbial communities under changing environmental conditions.</p>