Objective To investigate the association of cognitive function and clinical factors with electroencephalogram epileptiform discharges in benign childhood epilepsy with centrotemporal spikes (BECT). Methods The clinical data of children with BECT monitored by long-term video electroencephalogram from January 2019 to July 2022 were retrospectively analyzed, and the healthy children who underwent physical examination in outpatient department during the same period were selected as control group. Chinese Revised Wechsler Intelligence Scale for Children (C-WISC) test was conducted in both groups of children. The intelligence quotient of the two groups was compared, and the relationship between clinical factors, electroencephalogram epileptiform discharges and total intelligence quotient (FIQ), verbal intelligence quotient (VIQ) and performance intelligence quotient (PIQ) in children with BECT were analyzed. Results A total of 42 patients (18 boys and 24 girls) with typical BECT were included, with an average age of (9.4±2.0) years and an average onset age of (7.4±2.6) years. The control group consisted of 45 healthy children, including 28 boys and 17 girls, with an average age of (9.7±2.2) years. FIQ, VIQ, scores of classification and vocabulary in VIQ sub-items, as well as wood block map in PIQ sub-items in BECT group were lower compared with the control group, with statistical significance (P<0.05). FIQ and VIQ in <10-year-old group were lower than those in ≥10-year-old group among 42 children with BECT, and the differences was statistically significant (P<0.05). There was a statistically significant difference in VIQ among different discharge side groups (P<0.05), and the score of bilateral discharge group was lower. The onset age of children with BECT was significantly positively correlated with FIQ (r=0.39), VIQ (r=0.57) and scores of knowledge (r=0.49), classification (r=0.35), vocabulary (r_s=0.62), comprehension (r=0.43) and digit span (r=0.37) in VIQ sub-items. The course of disease was significantly negatively correlated with the scores of knowledge (r_s=-0.31) in VIQ sub-items (P<0.05). Compared with the group with onset age ≥10 years old, the scores of knowledge and vocabulary in VIQ sub-items in the group with onset age <10 years old were lower, and the difference was statistically significant (P<0.05). There were statistically significant differences in the scores of knowledge and digit span in VIQ sub-items among left, right and bilateral groups (P<0.05). Conclusions The average intelligence level of BECT children is in the normal range, but there is an imbalance in the intellectual structure, mainly manifested as impaired language function. Early onset age, bilateral cerebral hemispheres discharges and long course of disease are the main factors that affect the language function and lead to the decline of cognitive function in children with BECT.