Objective To investigate the correlation between obstructive sleep apnea hypopnea syndrome (OSAHS) and biochemical indexes in children. Methods Seventy-eight children with OSAHS in our hospital from January 2015 to February 2017 were recruited as an observation group, and 100 normal children who underwent physical examination were selected as a control group in the same period. The mean values and positive rates of biochemical markers were compared between two groups including alanine aminotransferase (ALT), blood urea nitrogen (BUN), total cholesterol (TC), triglyceride (TG), creatine kinase isoenzyme (CK-MB), cardiac troponin I (cTnI), fasting blood glucose (FPG) level. Results The mean values of biochemical indexes showed significant differences between the observation group and the control group except BUN and FPG [ALT, (52.1±26.2) U/L vs. (41.3±18.5) U/L; TC, (4.9±0.9) mmol/L vs. (4.3±0.8) mmol/L; TG, (1.4±0.7) mmol/L vs. (1.0±0.4) mmol/L; CK-MB, (24.3±9.5) U/L vs. (11.2±8.2) U/L; cTnI, (1.4±0.7) μg/L vs. (1.0±0.6) μg/L] (all P<0.05). The positive rates also showed significant differences between the observation group and the control group except BUN and FPG [ALT (48.7%vs. 14.0%), TC (24.4% vs. 8.0%), TG (23.1% vs. 8.0%), CK-MB (41.0% vs. 11.0%), cTnI (34.6% vs. 7.0%) (all P<0.05). Conclusions The cardiac function and liver function are significantly impaired in children with OSAHS, showing the disorder of lipid metabolism to some extent. These abnormal indexes may be the occurrence and development of OSAHS. More attention should be paid to the detection of biochemical indexes in children with OSAHS.