Objective To analyze the alteration of disease distribution and gender-differences of chronic non-communicable diseases (NCD) in hospitalized elderly from a large Comprehensive Hospital of Guangdong province. Methods Retrospective observational study including profile of discharged elderly in Nanhai hospital attached to Southern medical university from the year 2006 to 2014. Results In the top rank of diseases in hospitalized elderly, all were NCDs other than pneumonia and acute gastrointestinal diseases. The proportion of NCD accounted for all hospitalized elderly was reduced year by year, changed from 65.8% to 57.8%, P<0.01. Disease distribution of NCD altered obviously, showing that cerebrovascular disease (CVD) decreased from the first 21.3% to the second 17.0%, malignancy increased from 10.4% to 18.8% ranking as the first. Gender-differences did exist. Greater constituent ratio of chronic obstructive pulmonary disease (COPD) and malignancy were found in men than women yearly. NCD showed higher hospitalized expenses than non-NCD per capita, that of men were higher than women (P<0.05). Conclusion Summarizing the top and increasing rank of NCD and gender-differences in hospitalized elderly in a large comprehensive hospital, Nanhai district, Foshan city of 9 years, policy and program could be guided to optimize the distribution of medical resources and try to reduce the output of social economic burden.