The study was aimed at understanding the brain network and the change rule of brain neurotransmitter 5-hydroxytryptamine (5-HT) in autism children through resting-state electroencephalogram (EEG). 20 autistic children in hospital were selected and defined as the observation group. Meanwhile, 20 healthy children were defined as the control group. EEG signals were collected for the two groups. Fuzzy C-means (FCM) algorithm was used to extract features of EEG signals, and DTF was applied for the causal association between multichannel EEG signals. The two groups were compared for the average function value and regional efficiency of the brain neurotransmitter 5-HT. The results showed that the classification accuracy of frontal F7 channel, left frontal FP1 channel, and temporal T6 channel was 95.2%, 95.3%, and 91.2%, respectively. The average of high beta frequency band, low beta frequency band, theta frequency band, and alpha frequency band in the control group was significantly higher than that in the observation group under the optimal threshold (P < 0.05). Compared with normal subjects (34.27), the average function of 5-HT in the brain was 20.13 in patients with low function and 45.74 in patients with hyperfunction. In conclusion, FCM algorithm can feature extraction of EEG signals, especially in the frontal F7 channel, the left frontal FP1 channel, and the TEMPORAL T6 channel, which has high classification accuracy and can well express the EEG signals of autistic children. The level of 5-HT in autistic children is lower than that in healthy people, and it is closely related to loneliness and depression.