<b><i>Introduction:</i></b> This study aimed to evaluate whether endometriosis could disturb the mental health and health-related quality of life (HRQoL) of patients and to provide a new prospective for further treatment of endometriosis. <b><i>Methods:</i></b> A comprehensive literature review was conducted among 4 international databases (PubMed, Embase, Web of Science, and Cochrane Library) and 2 of the largest Chinese databases (the China National Knowledge Infrastructure and Wangfang). The Newcastle-Ottawa Scale was used to assess the quality of the included articles. Six effect sizes were synthesized through a meta-analysis, and a subgroup analysis was performed to identify potential moderating factors, including types of control groups, methods of assessment, number of study groups, and origin of the study. Potential publication bias was examined using a funnel plot. <b><i>Results:</i></b> This meta-analysis pooled 44 articles from 4 continents and 13 countries and compared 6 types of main effect sizes (the odds ratio [OR] for depression, the OR for anxiety, the standardized mean difference [SMD] for depression, the SMD for anxiety, the SMD for the physical component summary [PCS] and the SMD for the mental component summary [MCS]) between endometriosis patients and controls. Except for the SMD for depression, all other effect sizes revealed statistically significant differences between the study group and the controls. The main effect size outcomes of the subgroup analysis were also similar. The type of control group (<i>I</i><sup>2</sup> = 35% in non-endometriosis control groups for the SMD of anxiety; <i>I</i><sup>2</sup> = 47% in non-endometriosis control groups for the MCS of the 36-Item Short Form Health Survey) and the continent of origin (<i>I</i><sup>2</sup> = 0% in studies from South America for the OR of depression; <i>I</i><sup>2</sup> = 47% in studies from Europe for the SMD of anxiety) may influence heterogeneity in this analysis. Additionally, depression and anxiety symptoms in patients seemed to be more apparent compared with healthy controls when the sample was smaller and when a questionnaire was used. The publication bias of the articles was acceptable. <b><i>Conclusion:</i></b> Endometriosis can disturb mental health (specifically depression and anxiety) and decrease both the mental and physical HRQoL of patients. There may be some moderating factors that we were unable to identify in the subgroup analysis, but more research is necessary to develop proper management and improve the prognosis of endometriosis patients.