Genotypes-phenotypes correlation and treatment outcomes for 73 Chinese CHH male patients was performed in this study. Patients self-selected one of the four treatments: pulsatile Gonadorelin® pump, cyclical gonadotropins therapy, human menopausal gonadotropin monotherapy, or testosterone replacement treatment. Clinical assessments were performed every 3 months for 3 years. Baseline clinical features, spermatogenesis and secondary sexual development outcomes were analyzed. Whole exome sequencing identified 63 variants in 52 patients (70%), 18 of which were novel. Variants on FGFR1, PROKR2, CHD7, ANOS1 and NSMF gene were 10 (15.87%), 10 (15.87%), 7(11.11%), 5(7.93%) and 5(7.93%) respectively. Some null variants could lead to severe clinical manifestations than missense variants on FGFR1 and CHD7. The Lasso regression model for spermatogenic failure risk showed that cryptorchidism history, abnormal epididymis or prostate, lower basal LH and peak-LH post Triptorelin® stimulation were significant predictors. Approximately, 30% normosmic patients defined by simple olfactory assessment showed olfactory nerve center maldevelopment with nasal sinus MRI. The severity of reproductive system was attributed to spermatogenesis that could be predicted by nomogram model. No direct correlation was observed between candidate genes and spermatogenic outcome, however, the clinical severity is partially related with specific variants, and clinical features might in turn affect the treatment efficacy.