Speleothem 13C has been taken as an indicator of the history of rocky desertification, and changes in 13C have been thought to reflect the transition between C3 and C4 surface vegetation types. In this study the 13C values of plants, soil organic matter (SOM), dissolved inorganic carbon (DIC) of waters and modern calcite deposits in caves were investigated at five sites with different rocky desertification degree (RDD) in Southwest China. The main results can be summarized as follows:(1) dominant vegetation was the C3 type, with average plant 13C values ranging from 26‰ to 32‰(V-PDB), and SOM 13C values ranging from 20‰ to 25‰(V-PDB) for all the sites;(2) large variation for the 13C of DIC from drip water and modern calcite deposits in caves, which must be the result of multiple, inorganic factors in the epikarst zone and not the local vegetation type;(3) a proposed conceptual model to demonstrate that the evolution of Asian summer monsoon (ASM) can be recorded in speleothem 13C due to changes in epikarst zone hydrological conditions, exerting influence on stable carbon isotopes’ fractionation, and not necessarily due to changing vegetation types in the subtropical zone of Southwest China.