Developments in hyperspectral remote sensing techniques during the last decade have enabled the use of narrowband indices to evaluate the role of forest ecosystem variables in estimating carbon (C) fluxes. In this study, narrowband bio-indicators derived from EO-1 Hyperion data were investigated to determine whether they could capture the temporal variation and estimate the spatial variability of forest C fluxes derived from eddy covariance tower data. Nineteen indices were divided into four categories of optical indices: broadband, chlorophyll, red edge, and light use efficiency. Correlation tests were performed between the selected vegetation indices, gross primary production (GPP), and ecosystem respiration (Re). Among the 19 indices, five narrowband indices (Chlorophyll Index RedEdge 710, scaled photochemical reflectance index (SPRI)*enhanced vegetation index (EVI), SPRI*normalized difference vegetation index (NDVI), MCARI/OSAVI[705, 750] and the Vogelmann Index), and one broad band index (EVI) had R-squared values with a good fit for GPP and Re. The SPRI*NDVI has the highest significant coefficients of determination with GPP and Re (R² = 0.86 and 0.89, p < 0.0001, respectively). SPRI*NDVI was used in atmospheric inverse modeling at regional scales for the estimation of C fluxes. We compared the GPP spatial patterns inversed from our model with corresponding results from the Vegetation Photosynthesis Model (VPM), the Boreal Ecosystems Productivity Simulator model, and MODIS MOD17A2 products. The inversed GPP spatial patterns from our model of SPRI*NDVI had good agreement with the output from the VPM model. The normalized difference nitrogen index was well correlated with measured C net ecosystem exchange. Our findings indicated that narrowband bio-indicators based on EO-1 Hyperion images could be used to predict regional C flux variations for Northeastern China’s temperate broad-leaved Korean pine forest ecosystems.