This study aimed to conduct operation performance evaluations of Taiwan’s national hospitals during the period 2005–2008 and also propose appropriate suggestions for operation performance improvements. 28 national hospitals were selected as study objects and six input variables and three output variables were filtered as evaluation measures. Data envelopment analysis model was used for annual operation performance evaluation, and Malmquist productivity index for intertemporal operation performance change analysis. In addition, a performance scatter diagram and a strategy management matrix were utilized to synthetically analyze all kinds of operation performance data and accordingly improvement suggestions were proposed. Several findings were explored, including (1) nearly 60% of national hospitals ran an inefficient performance; (2) a significant gap between urban and nonurban hospitals did exist in health care resources allocation and medical service outputs, which reflected the negative public opinion about regional medical care resources gap in Taiwan; (3) other evidence depicted the expectation that the government of Taiwan has already wasted a lot of medical resources in the operation of Taiwan’s national hospitals; (4) 70–80% of Taiwan’s national hospitals ran a constant returns-of-scale operation, while the remainder ran a decreasing returns-of-scale operation; and (5) a extreme disparity existed in the total productivity, which rationally conjectured the cause came from the bad operation of several individual national hospitals. At last, two main suggestions advocated: (a) the government of Taiwan should reconsider the medical care resources allocation between urban and nonurban hospitals; and (b) hospital operation performance should be regarded as one of the main prerequisites for government budget subsidies so as to stimulate operation performance improvement and self-sufficiency operation.