The ongoing global warming is causing paddy soil to come under threat by hitherto unseen levels of carbon and nitrogen loss. The mechanism of soil organic matter (SOM) components and microbial metabolism responding to increased temperature is complicated; for example, the temperature sensitivity (Q10) of SOM decomposition in rice topsoil and subsoil remains poorly understood. In this study, 0–30 cm columns of undisturbed paddy soil were collected and incubated at 5, 15, or 25 °C for 117 days to investigate the effect of temperature on SOM decomposition and microbial characteristics in different soil layers. Results showed that Q10 of subsoil (15–30 cm) was more than twice that of topsoil (0–15 cm), indicating that SOM mineralisation in subsoil was facilitated more by temperature than that in topsoil. Warming promoted the decomposition of recalcitrant SOM and reduced the fluorescent intensity of dissolved organic matter. Increased temperature exerted no significant effect on microbial biomass, but it did enhance the relative abundance of oligotrophic bacteria and promote anabolism. Therefore, recalcitrant SOM decomposition driven by oligotrophic bacteria was more sensitive to warming than labile organic matter consumption mediated by copiotrophic bacteria. Our findings revealed the underlying mechanisms by which elevating temperature promoted SOM mineralisation, thereby emphasising the need to remain vigilant regarding the threat to carbon dynamics in deep soil poised by global climate changes.