Objective Fusarium wilt caused by Fusariumoxysporum f. sp. nivum is a typical soil-borne disease in watermelon production, posing significant threats. This study investigates the microbial community structures in the rhizosphere soil of healthy and Fusarium wilt-affected watermelon plants to clarify the regulatory effects of this disease on the physicochemical properties and microbial communities of rhizosphere soil. It aims to reveal the interactions between pathogen enrichment, beneficial microbial decline, and soil environmental factors, providing theoretical support for the green control of Fusarium wilt in watermelon plants by rhizosphere microbiome regulation. Methods Rhizosphere soil samples were collected from healthy plants (HT group) and Fusarium wilt-infected plants (FT group) of the watermelon variety ‘Xiaoyu No. 5’ in Shaoyang, Hunan. Physicochemical indicators including total nitrogen (TN), total phosphorus (TP), available phosphorus (AP), and available potassium (AK) were measured. Illumina high-throughput sequencing was employed to analyze the structures and diversity of microbial communities in the rhizosphere soil of healthy and disease-infected plants. Results The FT group had lower content of TP, AP, and AK in the rhizosphere soil than the HT group (P<0.05). The TN, organic matter (OM), and pH in the FT group were lower without significant differences than the HT group. The FT group had higher fungal ACE and Chao1 indices (P<0.05), higher bacterial ACE and Chao1 indices (P>0.05), and higher fungal and bacterial Simpson indices (evenness) (P<0.05) than the HT group. The abundance of Bacillota was significantly higher in the HT group than in the FT group, whereas that of Ascomycota was significantly higher in the FT group. At the genus level, the abundance of beneficial bacteria such as Neobacillus and Bacillus decreased in the FT group, while that of the pathogenic genus Fusarium increased sharply from 0.06% to 2.40%. The redundancy analysis (RDA) indicated that TN, TP, and OM were key drivers of bacterial community changes, whereas TN, OM, and AK were core regulators of fungal communities. Functional prediction suggested enhanced functions such as stress responses and energy metabolism of bacteria, alongside increased potential for functions such as plant cell wall degradation of fungi, in the diseased rhizosphere. Conclusion The occurrence of Fusarium wilt in watermelon plants leads to depletion of phosphorus and potassium in the rhizosphere soil and disrupts microbiome balance. This is manifested by the enrichment of Fusarium and the decline of beneficial bacteria (e.g., Neobacillus and Bacillus). Soil TN, OM, and AK are key environmental factors regulating this imbalance, with AK deficiency potentially serving as a pivotal link between soil environmental degradation and disease intensification. These findings provide crucial theoretical support for developing eco-friendly control strategies-potassium supplementation and stabilization alongside the targeted cultivation of beneficial microbial communities-targeting Fusarium wilt in watermelon plants.