Objective To analyze the relationship between viral load and clinical characteristics in children with infectious mononucleosis (IM) caused by Epstein-Barr virus (EBV). Methods A total of 128 children with IM who tested positive for EBV and admitted to our hospital from January 2016 to January 2021 were selected and divided into low virus group (n=64) and high virus group (n=64) according to their EBV level. The symptoms and signs, laboratory examinations and clinical characteristics of two groups were compared, and the correlation between the statistically different indicators and the amount of virus were analyzed. Results In children with high EBV level, the levels of alanine aminotransferase, lactate dehydrogenase, erythrocyte sedimentation rate, and peripheral blood white blood cell count were higher than low EBV level group (P<0.05). The time of fever, lymph node shrinkage, hepatosplenomegaly to subside, and hospitalization time of the children were all prolonged with the increase of EBV level (P<0.05). The level of EBV was positively correlated with the time to allay fever, the time to shrink the lymph nodes, the time to improve hepatosplenomegaly, and the length of hospital stay (r=0.453, 0.458, 0.402, 0.415,P<0.05). Conclusions The higher EBV level, the longer hospitalization time and recovery time of clinical indicators in children with IM. Therefore, the disease assessment of children with IM can be based on EBV level.