Objective To investigate the chronic diseases and comorbidity status in long-lived elderly (aged 90 years or older) in order to provide evidence for the management of multimorbidity in the patients. Methods Clinical data of 172 aged 90 years and over patients in the Research Center for Geriatrics of our hospital from January to December 2017 were collected and analyzed. Based on the presence of 25 most common chronic diseases (including geriatric syndrome), these chronic diseases and characteristic of multimorbidity were investigated. SPSS statistics 24.0 was used for statistical analysis. Intergroup comparison was performed with student′s t test or Chi-sqaure test depending on data type. Logistic regression analysis was adopted to analyze the actual and theoretical prevalence of diseases. Results Among the subjects, 156 (90.70%) of them had 2 or more comorbidities, with a mean number of (6.53±3.69). In the 25 screened chronic diseases, the top 5 with the highest prevalence were hypertension (128 cases, 74.42%), cerebrovascular disease (123 cases, 71.51%), coronary heart disease (91 cases, 52.91%), bone and joint disease (78 cases, 45.35%) and diabetes (70 cases, 40.70%). When 2 comorbidities were combined into a disease pair, the top 5 disease pairs were hypertension/benign prostatic hyperplasia (80 cases, 64.00%), hypertension/cerebrovascular disease (98 cases, 56.98%), cerebrovascular disease/benign prostatic hyperplasia (64 cases, 51.20%), hypertension/coronary heart disease (85 cases, 49.42%), and cerebrovascular disease/bone and joint disease (72 cases, 41.86%). The observed prevalence of specific disease pairs was higher than the expected prevalence, including hypertension/coronary heart disease (OR=2.452,95%CI 1.570-3.831), hypertension/benign prostatic hyperplasia (OR=2.757,95%CI 1.652-4.602), and coronary heart disease/cardiac insufficiency (OR=2.024,95%CI 1.249-3.280) (all P<0.05). Conclusion The incidence of chronic diseases and multimorbidity is quite high in long-lived elderly patients, and these multiple chronic conditions are associated.