Spectrally resolved fluorescence lifetime imaging 1-3 and spatial multiplexing 1,4,5 have offered information content and collection-efficiency boosts in microscopy, but efficient implementations for macroscopic applications are still lacking. An imaging platform based on time-resolved structured light and hyperspectral single-pixel detection has been developed to perform quantitative macroscopic fluorescence lifetime imaging (MFLI) over a large field of view (FOV) and multiple spectral bands simultaneously. The system makes use of three digital micromirror device (DMD)-based spatial light modulators (SLMs) to generate spatial optical bases and reconstruct N by N images over 16 spectral channels with a time-resolved capability (~40 ps temporal resolution) using fewer than N 2 optical measurements. We demonstrate the potential of this new imaging platform by quantitatively imaging near-infrared (NIR) Förster resonance energy transfer (FRET) both in vitro and in vivo. The technique is well suited for quantitative hyperspectral lifetime imaging with a high sensitivity and paves the way for many important biomedical applications. Optical imaging techniques are becoming central to the molecular investigation of samples at the macroscopic scale, with spectrally resolved imaging used to facilitate medical diagnosis 6,7 and operations, such as in guided surgery 8,9 , because of the spectrum-dependent nature of optical contrasts. Especially, MFLI offers the advantage of high sensitivity as well as the unmixing of spectra and of fluorescence lifetime-based biomarkers. As an intrinsic characteristic of a fluorophore and its state, fluorescence lifetime can be used to investigate the molecular environment (for example, pH, ion concentration, pO 2 , temperature) 10,11 with robustness because lifetime measurements are independent of intensity, which can be significantly altered by tissue heterogeneities and depth location. Spectrally resolved Reprints and permissions information is available online at www.nature.com/reprints.