In recent years, breakpoints (Bp) of muscle oxygenation have been measured in local muscles using near infrared spectroscopy (NIRS) to assess (predict) systemic aerobic capacity indices [lactate threshold (LT), gas exchange threshold (GET) and maximal oxygen uptake (VO_2peak)]. We investigated muscular differences in the assessment (predictive) ability of the Bp of muscle oxygenation for aerobic capacity indices during incremental cycling exercise on the aerobic capacity indices. Thirty-one active college students were recruited for an incremental cycling exercise test, during which NIRS muscle oxygenation in the vastus lateralis (VL) and gastrocnemius lateralis (GL), blood lactate concentration and cardiopulmonary variables were measured simultaneously in a multi-modality approach. A linear regression model was used to analyse the relationship between the Bp of the muscle oxygenation index (OI) and the systemic aerobic capacity indices. The Bp of the muscle OI in both the VL (BpVL) and GL (BpGL) were significantly correlated with the aerobic capacity indices. Additionally, the BpVL had a better goodness-of-fit [higher coefficient of determination (R², p < 0.001) and lower root mean squared error (RMSE, p < 0.03)] in the linear regressions and occurred earlier than the BpGL. In conclusion, both the BpVL and the BpGL could be measured by NIRS to assess the systemic aerobic capacity indices; however, there were muscular differences in the assessment ability of the Bp of muscle oxygenation.