With the Government’s full support and consolidation, the health care system in the territory of Taiwan has implemented National Health Insurance since 1995. The payment system transformed from “fee-for-service” to “prospective payment system” and finally to “global budgets”, and thereby made a material impact to the health care industry in the territory of Taiwan. According to the statistics of the Department of Health, the number of hospitals has declined from 823 in 1994 to 556 in 2005, with a declination rate of 32.4%. The medical treatments and health care services have a material influence to the public’s health. Meanwhile, due to the particular feature of the industry, it is intervened by governments throughout the world. Though in terms of the organizational theory, it is often defined as a non-profit-making organization in the business of service and its operation is subject to the government’s medical treatment policies and relevant laws. Therefore, notwithstanding that such services do not aim at making a profit as its first priority, they still should pay attention to the performance to upgrade the quality of service. This study purchased the database for “Report on 1996 and 2001 Industry, Commerce and Service Census Taiwan-Fukien Area, the Republic of China from the Directorate-General of Budget, Accounting and Statistics of the Executive Yuan. For the selection of the contents of hospitals, we obtained a total of 1,402 research samples. Using SPSS10.0 data analysis. The study result shows that in terms of such indexes as profitability, consolidated asset data, performance of application of assets, cost control and productivity, the ratio of fixed assets appears to be lower prior to the implementation of the National Health Insurance, while the ratio of current assets appears to be higher. Nevertheless, the turnover ratio of current assets appears to be higher upon the implementation of National Health Insurance, while the turnover ratio of fixed assets appears to be lower. Further, the profitability declined by approximately 50% after the implementation of National Health Insurance, and the ratio of increase in cost was higher than that of increase in income. Due to the implementation of National Health Insurance, it appears that each employee’s expenses were increased, and their productivity was increased relatively. According to the study on the characteristics of hospitals before and after the implementation of National Health Insurance, the implementa-tion of National Health Insurance produced a more significant impact on small-sized hospitals.