This study evaluates the sensitivity of major chronic diseases to the collapse of the healthcare system for developing prevention and control strategies under normal and emergency conditions. Data for the years 2018, 2019, and 2020 (coronavirus disease 2019 [COVID-19] pandemic) were curated from the National Disease Mortality Surveillance System, Chinese Center for Disease Control and Prevention for diseases such as cancer, heart disease (HD), cerebrovascular disease (CVD), and chronic obstructive pulmonary disease (COPD). The yearly death rate change for 2018, 2019, and 2020 were calculated. Similarly, expected and observed death cases, 95% confidence intervals, and Z-score were calculated for the year 2020 (COVID-19 pandemic). Furthermore, linear regression analysis was performed to analyze a correlation between the median age of various groups and the mortality rate. The observed death cases for cerebrovascular, heart, and other chronic diseases, were more than the expected death cases (430,007 vs 421,317, 369,684 vs 368,957, and 302,974 vs 300,366) as well as an upper limit of 95% confidence interval. The observed death cases for COPD and cancer are less than the expected death cases (127,786 vs 140,524, 450,346 vs 463,961) and lower limit of the 95% confidence interval. The highest Z-score was noted for cerebrovascular disease (105.14). The disease impact of severity was CVD, other chronic diseases, and HD in descending order. The unexpected decline in deaths was found for COPD and cancers with Z-scores (-166.45 and −116.32). The severity of impact was CVD, other chronic diseases, HD, cancer, and COPD in descending order. The COVID-19 pandemic has also resulted in an increase in deaths of the relatively young population as shown by the difference in rate of slop. The healthcare system collapsed due to prevention, control measures and increased burden of COVID-19 patients, affected chronic disease treatment/management and as a consequence variation in death rates occurs in different chronic diseases. A marked increase in mortality was observed in cerebrovascular disease. The unexpected decline in deaths from COPD and cancers, and increase in deaths of the relatively young population suggests that there may be opportunities for improvement in chronic disease management.