The aim was to analyze the application of computed tomography (CT) images in the diagnosis of lesions, and the composition of traditional Chinese medicine (TCM) syndromes in children with lobar pneumonia. Lung CT image registration algorithm was constructed based on optimized mean square deviation (OMSD) algorithm, which was applied to CT images of 188 children patients with lobar pneumonia before and after treatment. Besides, free-form deformation (FFD) algorithm and mean square deviation (MSD) algorithm were introduced for comparison with OMSD. Results showed that sum of squared differences (SSD) of OMSD was significantly lower than that of MSD and FFD (
P
<
0.05
). The mutual information (MI), relative overlap rate (ROR), and rcc of OMSD were markedly higher than those of MSD and FFD (
P
<
0.05
). After treatment, the number of pulmonary interstitial thickening, lobular interstitial thickening, ground-glass shadow, patchy shadow, consolidation shadow, pleural thickening, pleural effusion, lymphadenopathy, pneumothorax, and mediastinal emphysema decreased sharply in contrast to before treatment (
P
<
0.05
). Among the selected children, there were 184 children patients with empirical TCM syndrome, accounting for 97.85%, and its dominant syndrome was wind-heat closed lung syndrome (52.75%) and phlegm-heat closed lung syndrome (46.11%). The main symptoms of wind-heat closed and phlegm-heat closed lung syndrome were fever, cough, and pulmonary rales. In conclusion, OMSD was superior to MSD and FFD in lung CT image registration. CT registration image based on OMSD could clearly display the intrapulmonary and extrapulmonary manifestations of children patients, so as to enhance the clinical diagnosis effect. Besides, wind-heat closed lung syndrome and phlegm-heat closed lung syndrome were the common types of TCM syndrome of children pneumonia with the common symptoms of fever and cough.