Background and aims <p><i>Orobanche cumana</i> Wallr. is a holoparasitic weed that poses an increasing threat to sunflower cultivation. However, the influence of bio-organic fertilizers on <i>O. cumana</i>, remains inadequately understood. This study investigates the relationship between sunflower microbial community and <i>O. cumana</i> parasitism, as well as the inhibitory mechanism of bio-organic fertilizers on <i>O. cumana</i>.</p> Methods <p>Field investigation was conducted to study the response mechanisms of host microbial communities to parasitic plants using amplicon techniques. Pot experiment, the transcriptome was employed to investigate the mechanism by which bio-organic fertilizer inhibits <i>O. cumana</i> parasitism. Field experiments were conducted to explore changes in sunflower yield, quality and rhizosphere microecology.</p> Results <p>The results revealed rhizosphere bacterial community composition shifted notably with escalating parasite number. Bio-organic fertilizers application markedly upregulated the expression of <i>Mn-SOD</i>, <i>GST</i>, <i>XTH9</i>, <i>ACC01</i> and <i>NPR1</i> genes associated with plant resistance, and significantly increased the levels of the fruit ripening-related hormones ACC and tZTR. Application of bio-organic fertilizer remolded the rhizosphere microbial structure and significantly increased seed yield and crude protein content of sunflower. Upon applying bio-organic fertilizers, <i>O. cumana</i> roots exhibited decay-inducing fungal colonization, yet the isolated strain <i>Fusarium solani</i> L5 significantly reducing the number of parasites.</p> Conclusions <p>Bio-organic fertilizers demonstrated efficacy in suppressing <i>O. cumana</i> parasitism while enhancing sunflower productivity and quality. The results enhance our understanding of bio-organic fertilizers for controlling parasitic plants, offering insights into overcoming agricultural challenges through rhizosphere microbial communities.</p>