This study aimed to examine the mental health and social-emotional skills of individuals with mathematics difficulties (MD), reading difficulties (RD), and comorbid difficulties (MDRD) in China. Students with MD (n = 35), RD (n = 27), MDRD (n = 43), and typically-developing peers (TD, n = 167) completed the Children's Depression Inventory, the Children's Loneliness Questionnaire, the Social Anxiety Questionnaire, and the Survey on Social Emotional Skills (SSES). In regard to mental health, results showed that MDRD experienced significantly higher levels of loneliness compared to TD, while MD had significantly higher levels of depression than TD. No significant differences were found in mental health outcomes between the MD, RD, and MDRD groups. In regard to social-emotional skills, the results showed that MD had significantly lower levels of persistence, responsibility, self-control, emotional control, curiosity, and energy compared to TD. MDRD also showed significantly lower curiosity compared to TD. There were no significant differences in task performance, emotional regulation, collaboration, and open-mindedness among the MD, RD, and MDRD groups. These findings suggest that different learning difficulties are associated with distinct profiles of mental health and social-emotional skills.