This study aimed to explore the health-related quality of life (HRQoL) and subjective wellbeing (SWB) of infertility patients in mainland China and to investigate the relationships between HRQoL and SWB instruments in infertility patients. Methods We conducted this cross-sectional study in the Hospital for Reproductive Medicine Affiliated of Shandong University between April 2019 and November 2019. Participants self-completed the five-level EQ-5D (EQ-5D-5L) questionnaire, the Assessment of Quality of Life (AQoL)-8D, and the WHO-5 wellbeing index (WHO-5). The agreements between EQ-5D-5L and AQoL-8D were assessed employing intraclass correlation coefficient (ICC) and Bland-Altman plots. Exploratory factor analysis (EFA) was conducted to examine the difference in descriptive systems among the three instruments. Results We analyzed a valid sample of 618 infertility patients (84.4%). The mean scores of the total EQ-5D-5L, AQoL-8D, and WHO-5 were 0.96 (95%CI 0.96, 0.96), 0.80 (95%CI 0.79, 0.81), and 16.92 (95%CI 16.52, 17.31), respectively. Patients diagnosed with primary infertility had significantly lower HRQoL and SWB than those with secondary infertility. The ICC of EQ-5D-5L and AQoL-8D was 0.14. The AQoL-8D (r = 0.625) was more strongly correlated with WHO-5 than with the EQ-5D-5L (r = 0.262). The EFA results indicated that HRQoL instruments and the WHO-5 instruments were complementary rather than substitutable. Conclusions Poorer HRQoL and SWB were found that primary than secondary infertility patients. There exists a poor agreement between EQ-5D-5L and AQoL-8D and the difference in the psychosocial components may explain the difference. Measuring both HRQoL and SWB could provide complementary information for infertility patients.