Soil steam disinfection (SSD) technology is one of the effective means to eliminate soil-borne diseases, especially under the condition of clay-loam soil cultivation for facility agriculture in Yangtze River delta (China). With the fine particles, small pores and high density of the soil, the way of steam transport and heat transfer are quite different from those of other cultivation mediums, and when using SSD injection method, the diffusion of steam between pipes will be affected, inhibiting the heat transfer in the dense soil. Therefore, it is necessary to explore the influence of steam pipe spacing (SPS) on the energy consumption and soil temperature (ST) for clay-loam disinfection. The best results are to find a suitable SPS that satisfies the inter-tube steam that can be gathered together evenly without being lost to the air under limited boiler heating capacity. To this purpose, we first used a computational fluid dynamics model to calculate the effective SPS to inject steam into deep soil. Second, the ST, ST rise rate, ST coefficient of variation, and soil water content variation among different treatments (12, 18, 24, or 30 cm pipe spacing) were analysed. Finally, the heating efficiency of all treatments depending on the disinfection time ratio and relative energy consumption was evaluated. The result shows that in the clay-loam unique to Southern China, the elliptical shape of the high-temperature region obtained from the numerical simulation was basically consistent with the experiment results, and the ratios of short diameter to long diameter were 0.65 and 0.63, respectively. In the SPS = 12 and 18 cm treatments, the steam completely diffused at a 0–20 cm soil layer depth, and the heat transfer was convective. However, at an SPS = 12 cm, steam accumulation occurred at the steam pipe holes, causing excessive accumulation of steam heat. The relative energy consumptions for SPS = 30, 24, and 12 cm were above 2.18 kJ/(kg·°C), and the disinfection time ratio was below 0.8. Thus, under a two-pipe flow rate = 4–8 kg/h, the inter-tube steam was found to be completely concentrated with a uniform continuous high temperature distribution within the soil for an appropriate SPS = 18–22 cm, avoiding the unnecessary loss of steam heat, and this method can be considered for static and moving disinfection operations in the cultivated layer (−20–0 cm) of clay loam soil. However, for soil with higher clay contents, the SPS can be appropriately reduced to less than 18 cm. For soil with lower clay contents and higher sand contents, the SPS can be increased to more than 22 cm.