Presently, the effects of crop roots on crop root zone thermal characteristics are poorly understood, and new fertilizers are rarely considered from the perspective of changing crop root zone thermal characteristics. This study explored the effect of applying two new fertilizers, multiwalled carbon nanotubes (MWCNTs) and Bacillus atrophaeus (B. atrophaeus), on the crop root zone thermal characteristics of saline farmland soils through in situ measurements. The results showed that MWCNTs and B. atrophaeus could indirectly affect crop root zone thermal characteristics by changing the crop root growth. Combined application of MWCNTs and B. atrophaeus could promote both to induce positive effects, promote crop root growth, and significantly alleviate the adverse effects of soil salinization. The thermal conductivity and heat capacity of the shallow root zone were reduced due to the presence of crop roots, while the opposite was true in the deep root zone. For example, the thermal conductivity of the 0–5 cm rich root zone in the MWCNT treatment was 0.8174 W m−1 ·K−1, and the thermal conductivity of the poor root zone was 13.42% higher than that of the rich root zone. MWCNTs and B. atrophaeus can also change the spatial distribution of soil moisture, soil salt, and soil particle size characteristics by influencing the root-soil interactions and indirectly affecting crop root zone thermal characteristics. In addition, MWCNTs and B. atrophaeus could directly affect the root zone thermal characteristics by changing the soil properties. The higher the soil salt content was, the more obvious the effect of the MWCNTs and B. atrophaeus on the crop root zone thermal characteristics. The thermal conductivity and heat capacity of the crop root zone were positively correlated with the soil moisture content, soil salt content and soil particle specific surface area and negatively correlated with the soil particle size and the fresh and dry root weights. In summary, MWCNTs and B. atrophaeus significantly affected crop root zone thermal characteristics directly and indirectly and could adjust the temperature of the crop root zone.