The vertical heterogeneity of leaf biophysical and biochemical properties may have a large effect on the bidirectional reflectance and fluorescence of vegetation canopies. This has implications for the interpretation of remote sensing data. We developed a model for light interaction and energy balance in vegetation canopies in which leaf biophysical and biochemical properties vary in the vertical. The model mSCOPE is an extension of the Soil-Canopy Observation of Photosynthesis and Energy fluxes (SCOPE) model, which simulates spectral and bidirectional reflectance, fluorescence, and photosynthesis of vertically heterogeneous vegetation canopies. The modelling of radiative transfer in mSCOPE is based on the classical SAIL theory. A solution to the radiative transfer equation for multi-layer canopies is given, which allows calculating top-of-canopy (TOC) reflectance and the flux profile. The latter is used for the simulation of fluorescence emission and photosynthesis of every leaf through the leaf radiative transfer model Fluspect and a biochemical model. The radiative transfer of fluorescence in multi-layer canopies is solved numerically in mSCOPE to obtain TOC bidirectional fluorescence. The significant effect of vertical heterogeneity of leaf properties on TOC reflectance, fluorescence and photosynthesis is demonstrated by different scenarios with customized vertical profiles of leaf chlorophyll content and leaf water content, and also with measured vertical profiles of leaf chlorophyll content in corn canopies. A preliminary validation of the reflectance calculating routine of mSCOPE is conducted by comparing measured and simulated TOC reflectance spectra of the corn canopies. We conclude that it is important to consider the vertical heterogeneity of leaf properties for the prediction of reflectance, fluorescence and photosynthesis. The model mSCOPE could serve as a tool to better understand vertically heterogeneous vegetation canopies.