Abstract: The karst region in Southwest China is one of the most ecologically fragile areas characterized with severe rocky desertification, and increased and frequent flood events. Vegetation restoration has been recognized as an effective strategy for soil carbon and nitrogen accumulation in degraded ecosystems. However, soil carbon and nitrogen dynamics following vegetation restoration have not been evaluated with a long-term, fixed-point research approach in the karst areas. Thus, we compared the effects of vegetation restoration types on soil carbon and nitrogen stocks before (in 2004) and after 10 (in 2014) and 13 years (in 2017) of cropland abandonment. Four restoration strategies were implemented in the present study, namely, restoration with plantation forest, grassland, a combination of plantation forest and grassland, and spontaneous regeneration to a natural grassland. Cropland under maize-soybean rotation (CR) was used as the control. From 2004 to 2014, there were no extreme water-logging disasters, whereas from 2014 to 2017, two extreme water-logging disasters occurred in the study region. The results revealed that soil organic carbon (SOC) stocks in all the four restored vegetation types significantly increased after 10 years of cropland abandonment, whereas after 13 years, the plantation forest, grassland, and the combination of plantation forest and grassland, except the natural grassland, showed a decreasing trend. The increase in the total nitrogen (TN) content of soil in response to vegetation restoration was less than that of SOC; the TN content significantly increased only in the grassland after 10 years of cropland abandonment. The TN content in the combination of plantation forest and grassland and natural grassland increased after 13 years of cropland abandonment, and that in the natural grassland continuously increased after cropland abandonment. The correlation analysis showed that soil exchangeable Ca²⁺ was positively correlated with SOC and TN (P < 0.05). However, the content of soil exchangeable Ca²⁺ significantly decreased in 2017 than in 2014. The reduction in soil exchangeable Ca²⁺ can be attributed to the continuous flood event in the study area in 2015 and 2016. Vegetation restoration can significantly improve soil carbon and nitrogen sequestration in karst areas. Furthermore, when compared with other vegetation restoration types, natural vegetation restoration was more beneficial to soil carbon and nitrogen sequestration, which can resist the negative effects of extreme climate disasters effectively.