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A discussion is conducted on the problems of ideological and political education, rotation learning in departments, clinical and scientific research capabilities, paper writing, and improvement of the quality of papers encountered by professional master of clinical medicine in the “two-track integration” mode during the standardized training of resident doctors. On that basis, several methods are proposed in the present study (e.g., stressing ideological education for professional masters, coordinating learn of professional skills, enhancing paper writing ability and scientific research ability, organizing a professional team of tutors). On that basis, this study summarizes the problems and challenges exposed in training professional medical students, especially under “two-track integration” mode, seeks to propose a novel idea to serve better for the “two-track integration” educational mode, including provide solutions to help students establish learning goals, to enhance their writing ability, to narrow the bridge between teachers and students, etc. All of which, aims to optimize the training of professional masters of clinical medicine, and give some feasible suggestions for subsequent research. Hopefully, the suggestions and proposal in this study would draw attention and serve better to increase the education quality on professional medical students.