Capsanthin is the major natural carotenoid pigment in red chili pepper possessing important bioactivity. Its conventional determination method is high performance liquid chromatography (HPLC) with complex and tedious sample pretreatment. In this study, synchronous front-face fluorescence spectroscopy (FFFS) was applied for the fast and non-invasive detection of free capsanthin in chili powders. Although capsanthin was only weak fluorescent in solution state, it showed strong fluorescence in two separated regions in front-face geometry which could also be clearly observed in chili powders. The mechanisms of these emissions are revealed to be aggregation-induced emission (AIE) and J-aggregate formation (JAF). The free capsanthin in 85 chili powder samples were determined by HPLC as in the range of 0.6–3.0 mg/g. The total synchronous FFFS spectra of these samples were scanned. Simple first-order models were built by partial least square regression (PLSR), and were validated by 5-fold cross-validation and external validation. The coefficients of determination (R2) were higher than 0.9, and the root mean square errors (RMSE) were less than 0.2 mg/g. The relative error of prediction (REP) was 9.9%, and the residual predictive deviation (RPD) was 3.7. The method was applied for the estimation of free capsanthin in several real-world samples with satisfactory analytical results. The average relative error to HPLC reference values was −11.8%.