The effect of exotropia on the intelligence of children is unknown. This study aimed to assess the intelligence in children with exotropia and investigate the influence of the main clinical indexes of strabismus on intelligence. Eighty-four participants aged 8–12 years were enrolled, including 37 patients with exotropia (exotropia group) and 47 normal individuals (normal group). Intelligence was assessed by the Wechsler Intelligence Scale for Children—Fourth Edition (WISC-IV), including the Verbal Comprehension Index (VCI), Perceptual Reasoning Index (PRI), Working Memory Index (WMI), Processing Speed Index (PSI), and Full-Scale Intelligence Quotient (FSIQ). The exotropia group had a significantly lower PRI score but a higher PSI score than the normal group. However, there was no significant difference in the WMI, VCI, and FSIQ between groups. Multiple linear regression showed that PRI–WMI and PRI–PSI differences were significantly lower in the exotropia group. Inter-subscale correlations analysis showed that the pattern of intelligence structure was different between groups. The type of exotropia, angle of deviation, duration of symptoms, and stereoacuity had no effect on the intelligence of children with exotropia. Children with exotropia had a relatively worse performance in the perceptual reasoning skill but a better processing speed and a different pattern of intelligence structure.