As a significant part of people’s self-concept, gender identity refers to people’s self-understanding of their gender based on social or cultural expectations. According to the two-dimension model of gender identity, masculinity and femininity are two independent dimensions of gender identity, and self-rating and subordinate-rating are two principal approaches using questionnaires (such as BSRI) to evaluate leaders’ gender identity, self-rating and subordinate-rating. However, by using these two rating methods, researchers often reach different result. Hence, this study firstly tried to find out whether there are any substantive differences between self-rating and subordinate-rating in leaders’ gender identity. In the studies of gender identity and leadership, gender role congruity perspective was always the choice of researchers as their theoretical basis. However, since both target stimulus’ (leader’) and perceivers’ (subordinate’) characteristics play important roles in leadership perception, it is insufficient to consider such research mainly from the target stimulus’s (leader’s) perspective. Thus, this study adopts the implicit leadership theory and stands on both leaders’ and subordinates’ sides to explore the influences of leaders’ sex and subordinates’ sex. Based on the implicit leadership theory, this study explores three differences in the evaluation of leaders’ gender identity, which are the differences between self-rating and subordinate-rating in leaders’ gender identity, the subordinate-rating differences between male leaders and female leaders in leaders’ gender identity, and the differences between male subordinates’ rating and female subordinates’ rating in gender identity of leaders. By using a matched questionnaire survey, this research collects 70 valid department samples (including 70 leader samples and 230 subordinate samples) from employees of the Chinese government and government-affiliated institutions. Specifically, leaders are asked to rate their own gender identity, while subordinates are asked to rate their department managers’ gender identity. The results are as follows: (1) subordinates tends to overestimate the masculinity component of leaders’ gender identity compared with leaders’ self-rating, while there is no significant difference between leader-rating and subordinate-rating in femininity dimension; (2) subordinates’ rating of male leaders’ masculinity is significantly higher than that of femininity, while there is no significant difference between masculinity and femininity when evaluating female leaders; (3) male subordinates rate higher than female subordinates in the masculinity component of leaders’ gender identity, while male and female subordinates’ evaluation of femininity is almost the same. In summary, this study explores three differences in leaders’ gender identity ratings based on the implicit leadership theory, which may not only contribute to theory development for future research but shed light on the internal mechanism exploration. Also, this study gives some suggestions to both leaders and organizations. For leaders, depending on their sexes and organizational types, they can shape their behaviors to make themselves match with subordinates’ prototype; for organizations, when they choose or promote a leader, they need to consider whether a candidate comprehensively fit with their organizations’ leadership prototype. Therefore, a leader or organization can be much more effective.