In this research, we analyzed the impact of waterlogging stress on the soil invertase activity (SIA), soil urease activity (SUA), maize growth-related indicators and maize yield-related indicators, and obtained the correlations between them. Results showed that waterlogging stress has different degrees of negative effects on the two enzyme activities, as well as most of maize growth-related/yield-related indicators. The negative effect is intensified with the increase of flooding depth or duration, and the flooding depth had a greater effect than the flooding duration. Compared with the treatment of no waterlogging control (treatment CK), the treatment of waterlogging lasting 4 d with depth of 15 cm (treatment H3T2) resulted in a decrease of SIA by 44.1% (1 d), 29.7% (7 d) and 21.4% (21 d), and reduced SUA by 25.8% (1 d), 21.5% (7 d) and 10.3% (21 d), respectively. The waterlogging adversely affected the yield of maize. Kernel dry weight (KDW) is directly related to corn yield, and decreased by 18.5% compared with treatment CK. SIA and SUA showed strong positive correlation with most growth-related/yield-related indicators, but SUA showed a slightly stronger correlation with these indicators than SIA. Among 10 indicators, there were 8 indicators whose correlation coefficient with SIA exceeded 0.8, accounting for about 80%. There were 9 indicators whose correlation coefficient with SUA exceeded 0.8, accounting for about 90% of the 10 indicators. In cluster analysis, KDW of waterlogging stress was prioritized into four main clusters. The flooding depth of 10 cm (H = 10 cm) and the flooding duration of 4 d (T = 4 d) were regarded as critical point in the study.