Ear rot is one of the most destructive diseases found in the major corn-producing areas of China and worldwide. The disease reduces the quality and yield of corn, and the mycotoxin adversely affects human and animal health. The present study explored the genetic diversity, pathogenicity, and toxigenicity of two dominant Fusarium species (Fusarium verticillioides and Fusarium proliferatum) in the summer-sown regions of China. We identified 1349 Fusarium isolates, including F. verticillioides (71%), F. proliferatum (21%), Fusarium graminearum (6%), and Fusarium oxysporum (2%), in the maize ear rot samples collected between 2019 and 2020 from the summer-sown areas of China. The F. verticillioides isolates from Henan showed high aggressiveness (30.6), and fumonisins production ability (FB1, 3087.8 µg/kg; FB2, 1546.8 µg/kg). Field pathogenicity test in Hefei and Linquan showed that all isolates caused ear rot, with varying levels of pathogenicity. F. verticillioides isolates demonstrated higher pathogenicity than F. proliferatum in the summer-sown areas of China except for the Shānxī region. Meanwhile, the F. proliferatum isolates from Anhui showed the highest genetic diversity, genotypes, aggressiveness (28.5), and Fumonisins production ability (2816.1 µg/kg FB1; 1268.7 µg/kg FB2). Based on the disease (ear rot) severity index, the study also classified the isolates as low, medium, and highly aggressive. The ability to produce fumonisins (FB1 and FB2) in maize also varied among the different F. verticillioides and F. proliferatum isolates; F. verticillioides produced 162.9–7545.5 µg/kg of FB1 and 43.2–3831.9 µg/kg of FB2, while F. proliferatum produced 282.0–5678.8 µg/kg of FB1 and 118.2–3741.7 µg/kg of FB2. Furthermore, a significant positive correlation was detected between pathogenicity and FB1 and FB2 production (r > 0.74, P < 0.01). These findings improve our understanding of the maize ear rot pathogenic and their potential risks to human and animal health. The study thus provides a theoretical basis for the comprehensive prevention and control of maize ear rot in the summer-sown regions of China.