Objective To summarize and analyze the screening results, treatment and follow-up of hyperhenylalaninemia (HPA) and congenital hypothyroidism (CH) in neonatal screening center of Shaanxi province from 2010 to 2016.Methods Newborn fetus heel blood was collected 72 hours after birth, and dried blood filter paper was made. The levels of phenylalanine (Phe) and thyrotropin (TSH) were tested, and patients with positive results of Phe ≥2.0 mg/dl、TSH ≥10 μU/ml were recalled for diagnosis. The blood levels of Phe and Tyr were detected by tandem mass spectrometry (MS/MS), and thyroid function (TSH,T₃,T₄, FT₃, FT₄) was detected and analyzed by chemiluminescence immunoassay, so that the diagnosed was made.Results The number of live births in the province′s midwifery institutions was 2 751 268 cases from 2010 to 2016, 2 329 335 (84.67%) cases were screened. Totally 131(1/17 781), 300 (1/7 764), 966 (1/2 411) cases were diagnosed with mild HPA, phenylketonuria (PKU) and CH, respectively. Medical records were established after the diagnosis, and participants were given low-phenylalanine diet and oral levothyroxine tablets (L-T₄) alternative treatment. Gesell Developmental Scale assessment results indicated that PKU children who started treatment within 6 months of age had significantly higher intelligence quotient (IQ) than those who started treatment after 6 months of age (P<0.01). Follow-up monitoring indicated that there was no significant difference on IQ between CH children and normal children after sustained treatment (P>0.05).Conclusion Comprehensive screening of neonatal diseases, increasing screening coverage, standardization of treatment and long-term follow-up monitoring as soon as possible can prevent PKU and CH children from irreversible impairment of physical and mental status, which is of great significance in improving their prognosis and quality of life.