The purpose of this study was to explore the current situation of civil servants’ perception of organizational justice and morale in physical education administrative organizations, and analyze the relationship between them. This study employed the questionnaire method. 336 civil servants in physical education administrative organizations were selected as samples, with the return of 177 questionnaires. The amount of the valid questionnaires stands for 52.68% of the total amount of the questionnaires those were distributed. According to the results of the data analysis, the main conclusions were as follows: 1. Civil servants’ perception of organizational justice appear middle level influence. 2. Civil servants’ morale was at upper middle level. 3. Civil servants’ perception of organizational justice was affected by seniority and rank. 4. Civil servants’ morale was affected by gender and rank. 5. Civil servants’ perception of organizational justice appear positively influence to their morale. 6. Parts of civil servants’ perception of organizational justice had significant predictability on their morale.