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Soil steam disinfection offers a chemical-free solution to soil-borne pathogens and continuous cropping obstacles; however, its adoption in facility agriculture is severely limited by the lack of mobile and efficient steam generation systems. Conventional electric or coal-powered boilers are too bulky and immobile for practical field application. To bridge this technological gap, this study developed an optimized gasoline-powered steam boiler utilizing an innovative Helmholtz-type pulse combustion system. Key components, including a dual-carburetor Y-shaped throat and a helical tailpipe configuration, were designed to enhance compactness and thermal efficiency—achieving a 67.11% reduction in length and 204% increase in heat transfer area compared to a straight pipe equivalent. Computational fluid dynamics simulations systematically optimized the spatial arrangement of four pulse combustors, revealing layout as a critical performance factor. The optimal configuration reduced water heating time to 407.1 s, 15.52 s faster than the average across 12 designs. Field validation demonstrated that a double-layer steam injection needle significantly improved thermal retention, maintaining soil temperatures ≥80°C for 63.84 minutes—27.02% longer than a single-layer design following 6 minutes of steam injection. These findings confirm the system’s efficacy in delivering lethal thermal dosage to soil pathogens. This work not only provides a practical mobile soil steam disinfection solution but also advances fundamental insights into the design of efficient thermal fluid systems for agricultural applications.