Abstract: This paper explored the effects of deep vertical rotary tillage and rice straw overturning on soil physicochemical properties, organic carbon fractions and carbon pool management index (CPMI) and their driving factors through field experiments and indoor analysis methods, and set up the three treatments including rotary tillage + rice straw removed (LT), rotary tillage + rice straw return (XG), and vertical rotary tillage + rice straw overturning (ZF). The results showed that: (1) Compared with LT and XG treatments, ZF treatment significantly decreased soil bulk density (BD), increased soil total and capillary porosity (TP) and capillary porosity (CP), enhanced the content of total organic carbon (TOC), available nitrogen (AN) and available potassium (AK) and increased the content of soil particle carbon (POC) and easily oxidizable carbon (EOC), SOC stability and CPMI. (2) The RDA analysis showed that BD, TP and CP were mainly soil physicochemical indices affecting SOC and its fractions, SOC stability and CPMI and TOC, POC, POC/TOC, EOC/TOC, and Kos were SOC indicators directly affecting CPMI. (3) The results of SEM showed that ZF increased soil TOC and POC content indirectly by input of organic matter and directly by reducing BD and increasing TP and CP. The increase in soil TOC and POC content elevated the stability of SOC and the CPMI. Therefore, ZF was conducive to improving the quality of tobacco-planting soil.