Through potted plant experiments, drought tolerance of 14 cassava cultivars at seedling stage under water stress was measured. Comprehensive principal components analysis, cluster analysis and correlation analysis showed that the drought tolerance coefficient (DTC) of peroxidase (POD) activity, soluble protein content (Pr) content, malondialdehyde (MDA) content, free proline (Pro) content, plant height and stem diameter were 0.14–4.00，0.12–3.28，0.55–1.76，0.33–1.70， 0.68–1.09 and 0.62–1.05，respectively. POD activity showed the largest correlation coefficient with F value (the comprehensive analysis), followed by Pr content，plant height，stem diameter，Pro content and MDA content. POD activity and Pr content were very significantly positive correlated to F value，and there was very significantly positive correlation between POD activity and Pr content. After comprehensive comparison, POD activity and Pr content were recommended as the main indexes for evaluation of drought tolerance of cassava seedlings.