Objectives The methods of certificating course with process-based assessment under the two apprenticeship systems were studied by organically integrating the modern apprenticeship system with the new apprenticeship system in enterprises to help to evaluate effect of teaching, achieve goals of training talents, and improve the quality of talent trained. Methods The college cooperated with several enterprises. The enterprises adopted a mentorship approach to instruct apprentices while the college was responsible for training employees from enterprises based on programs of training talents. The practice of skills for job seeking and the learning of theoretical knowledge was conducted with two-way cooperation to promote the deep integration of joint education between colleges and enterprises. Results Both the college and enterprises jointly developed a program of training talents in group of major based on the rules of training technical and skilled talents and the requirements of career in the group of animal husbandry and veterinary majors. The system of courses in group of majors was studied and practiced. The process-based assessment and evaluation was conducted. The plans of process-based assessment under the two modes were developed. Conclusions The practice of process-based assessment under the modern apprenticeship system and new apprenticeship system in enterprises helps to check the effect of teaching, achieve the goals of training talent, improve the quality of talents trained, and promote the reform of majors.