The curriculum moral education of science courses of universities closely related to training direction of Chinese talents is an important guarantee realizing national goal of fostering virtue through education. The paper outlines political environment and significance of carrying out a curriculum moral education for science courses in the new era. By a status analysis of the curriculum moral education for science courses of Nanjing University, the author pointed out some shortcomings and issues concealing in the recent moral education of science courses of universities, and proposed constrictive suggestions and measures for improving and promoting the building of long-term mechanism of moral education for science courses of universities in the new era.