The purpose of this study was to explore the current situation of civil servants' job stress and working burnout in physical education administrative organizations, and analyze the relationship between them. This study employed the survey method. Three hundred and thirty-six civil servants in physical education administrative organizations were selected as samples, with the return of 189 questionnaires. The amount of the valid questionnaires stands for 56.25% of the total amount of the questionnaires those were distributed. The survey data was analyzed by using statistical methods. The findings of the study are as follows: (1) Civil servants in physical education administrative organizations feel that their job stress is at upper middle level. (2) Civil servants in physical education administrative organizations feel that their working burnout is at middle level. (3) The perception of job stress was affected by gender and seniority of civil servants in physical education administrative organizations. (4) The perception of working burnout was affected by marriage status and seniority of civil servants in physical education administrative organizations. (5) Significant canonical correlation was found between civil servants' job stress and working burnout. (6) Some parts of civil servants' job stress have significant predictability on civil servants' working burnout. In the end, based on the findings and conclusions of this research, some suggestions were given to physical education administrative organizations' authorities for reference.