Members of the Fusarium graminearum species complex (FGSC) are important pathogens on wheat, maize, barley, and rice in China. Harvested grains are often contaminated by mycotoxins, such as the trichothecene nivalenol (NIV) and deoxynivalenol (DON) and the estrogenic mycotoxin zearalenone (ZEN), which is a big threat to humans and animals. In this study, 97 isolates were collected from maize, wheat, and rice in Jiangsu and Anhui provinces in 2013 and characterized by species- and chemotype-specific PCR. F. graminearum sensu stricto (s. str.) was predominant on maize, while most of the isolates collected from rice and wheat were identified as F. asiaticum. Fusarium isolates from three hosts varied in trichothecene chemotypes. The 3-acetyldeoxynivalenol (3ADON) chemotype predominated on wheat and rice population, while 15ADON was prevailing in the remaining isolates. Sequence analysis of the translation elongation factor 1α and trichodiene synthase indicated the accuracy of the above conclusion. Additionally, phylogenetic analysis suggested four groups with strong correlation with species, chemotype, and host. These isolates were also evaluated for their sensitivity to carbendazim and mycotoxins production. The maize population was less sensitive than the other two. The DON levels were similar in three populations, while those isolates on maize produced more ZEN. More DON was produced in carbendazim resistant strains than sensitive ones, but it seemed that carbendazim resistance had no effect on ZEN production in wheat culture.