Modification of cell cycle in entomopathogenic fungi is likely crucial for host infection and environmental adaptation. Here we show that Wee1 and Cdc25 can balance cell cycle-required cyclin-dependent kinase 1 (Cdk1) activity in Beauveria bassiana. The Cdk1 phosporylation signal was strong in Δcdc25 but very weak in Δwee1 and absent in Δwee1Δcdc25. Consequently, cell cycles, septation patterns and many septation-dependent gene transcripts of these mutants were reversely changed. Hyphal cells were short in Δwee1, slender in Δcdc25 and short and swollen in Δwee1Δcdc25. Conidiation was most defective in Δwee1, followed by Δcdc25. Their conidia and yeast-like blastospores also altered antagonistically in both size and complexity, accompanied with abnormally branched germlings in Δwee1 and Δwee1Δcdc25. Conidial thermotolerance and UV-B resistance decreased much more in Δwee1Δcdc25 than in Δwee1 but significantly increased in Δcdc25. The double deletion and the point mutation Cdk1(T14A/P15F) for inhibitory phosphorylation caused most defective virulence, followed by wee1 deletion. All the changes were restored by ectopic gene complementation. Virulence changes in all the mutants and control strains were highly correlated to those in blastospore size or complexity. Taken together, Wee1 and Cdc25 control cell cycle, morphogenesis, asexual development, stress tolerance and virulence of B. bassiana by balancing the Cdk1 activity.