Jackfruit (Artocarpus heterophyllus) is an important economic crop in tropical and subtropical regions, especially in South and Southeast Asia. In recent years, trunk canker disease caused by Phytophthora palmivora has emerged as a major threat to jackfruit production. To explore sustainable alternatives to chemical control, this study investigated the antagonistic potential of Bacillus rhizobacteria. Four Bacillus sp. strains (CT1, CT2, CT3, and CT4) were isolated from 12 jackfruit rhizosphere soil samples from jackfruit fields in Chau Thanh commune, An Giang province, Viet Nam. Morphological characterization was performed, followed by in vitro antagonism assays against Phytophthora sp. One strain exhibiting the highest inhibition activity was selected for ITS gene sequencing and enzymatic profiling. The results showed that all were gram-positive, catalase-positive, KOH-negative, and showed antifungal activity. Among them, the strain identified as Bacillus velezensis CT4 exhibited the most stable antagonistic effect (17.8–73.7%) and the strongest production of cellulase (33.4–64.2 mm), β-glucanase (40.7–68.8 mm), and protease (45.5–65.7 mm) from 3 to 9 days after the test. Bacillus velezensis CT4 was considered a promising biocontrol agent for managing trunk canker disease, with the potential for commercial applications or scalability in jackfruit.