Objective. This study is aimed at researching transcranial magnetic stimulation (TMS) effects combined with computer-aided cognitive training (CACT) on cognitive function of children suffering from cerebral palsy and dysgnosia. Methods. From December 2019 to October 2021, 86 children with cerebral palsy and dysgnosia who were treated at our hospital were recruited and assigned into observation and control groups (
n
=
43
, each) using the random number table technique. The observation group received TMS combined with CACT (TMS+CACT), whereas the control group received only TMS. Chinese Wechsler Young Children Scale of Intelligence (C-WYCSI) and Chinese-Wechsler Intelligence Scale for Children (C-WISC) were used to evaluate the intelligence level of the two groups; Gross Motor Function Measure-88 (GMFM-88) of Fudan Chinese version was employed for evaluating the gross motor function of the two groups; a comparison was drawn among the two groups for the cerebral hemodynamic parameters before and after the treatment. Results. For young children, the verbal intelligence quotient (VIQ) scores at 6 and 12 weeks of treatment in the observation group were increased when compared to those in the control group (
48.91
±
3.70
vs.
47.32
±
3.33
,
54.25
±
4.46
vs.
49.48
±
3.36
), and the observation group’s performance intelligence quotient (PIQ) score at 12 weeks of treatment was higher as to that of the control group (
65.38
±
4.23
vs.
62.81
±
4.74
, all
P
<
0.05
). For older age children, the observation group’s VIQ and PIQ scores were greater than the control group’s at 6 and 12 weeks of treatment, with statistical significance (
63.80
±
3.76
vs.
59.50
±
5.32
,
74.64
±
12.04
vs.
65.08
±
6.30
;
63.91
±
5.96
vs.
58.42
±
3.70
,
72.73
±
5.06
vs.
66.42
±
5.93
; all
P
<
0.05
). The GMFM-88 scale scores in both groups were increased after 6 and 12 weeks of treatment. After treatment for 12 weeks, the observation group’s A-E scores were greater than those of the control group (all
P
<
0.05
). The peak systolic velocity (
V
s
), end-diastolic velocity (
V
d
), and mean velocity (
V
m
) at the anterior cerebral artery (ACA), middle cerebral artery (MCA), and posterior cerebral artery (PCA) in the observation group were dramatically increased than those in the control group (all
P
<
0.05
) after 12 weeks of treatment. Conclusion. TMS+CACT can effectively improve the intelligence level, cognitive ability, gross motor function, and cerebral blood flow of children suffering from cerebral palsy and intellectual disability.