The invention provides a time-resolved extreme-low-light multispectral imaging system and method and belongs to the field of extreme-low-light multispectral imaging, wherein the system is triggered through a trigger to ensure the time-resolved property, and the multispectral high-resolution two-dimensional color imaging for extreme-low-light objects is realized by combining a triggering technology of the trigger, the compressive sensing theory, a DLP (digital light processing) technology, a spectrum-dividing technology, an optical fiber coupling technology and a photon counter linear array detection technology; the system is composed of an extreme-low-light light source or self-luminous organisms, the trigger, an optical filter, an optical imaging system, a DMD (digital mirror device) micromirror array, an optical focussing and collecting system, a spectrophotometer, a photo counter lineary array consisting of a plurality of photon counters with different wavelengths, a driving control module and an optimization algorithm module; the sensitivity of the system can reach the level of a photon, and can be widely applied to the fields of self-luminous organism detection, medical treatment imaging, data acquisition, communication, astronomy, military, hyperspectral imaging, measurement in quantum mechanics and the like.