Focusing on the implementation of the National Medium- and Long-Term Program for the Development of Science and Technology (2006-2020), a comparative analysis of the science, technology and innovation levels of China and major innovative countries is conducted from six dimensions including R&D funding, R&D personnel, papers, patents, knowledge-intensive industries, and innovators. The great progress that China has made for the past 15 years is summarized. China has become the world's second largest R&D investment country, the number of highly cited scholars has jumped to the second place in the world. The numbers of highly cited papers, applied and granted patents have grown rapidly to the top in the world, the scale of knowledge-intensive industries and their exports have maintained rapid growth. On the other hang gaps and deficiencies in China's R&D investment structure, top talents, technological competitiveness, etc are revealed. The R&D intensity has not exceeded the critical point of 2.5% and the proportion of basic research investment is still significantly low. The number of R&D researchers is small and the growth is very slow. The proportion of corporate R&D personnel has generally shown a slight-downward trend. In terms of patent quality, there is still a significant gap between China and the United States, Japan, Germany and South Korea. Innovation activities are still limited to a few companies and innovative leading companies are scarce. Several suggestions are proposed in terms of diversified investment, talent training and gathering, effective supply of core technologies, and equal attention on quantity and quality indicators.