The vertical structure of vegetation canopies creates micro-climates, which can substantially affect ecosystem responses to climate change. However, the land components of most Earth System Models, including the Energy Exascale Earth System Model (E3SM), typically neglect vertical canopy structure by using a single layer big-leaf representation to simulate water, \cotwo, and energy exchanges between the land and the atmosphere. In this study, we developed a standalone Multi-Layer Canopy Model (MLCMv1) for the E3SM Land Model (ELM) to resolve the micro-climate created by vegetation canopies. The support for the heterogeneous computation architectures is included by using the Portable Extensible Toolkit for Scientific Programming. The numerical implementation of ELM-MLCMv1 was verified against CLM-ml\_v1 for a month-long simulation using data from the Ameriflux US-University of Michigan Biological Station (US-UMB) site. Model structural uncertainty was explored by performing control simulations for five stomatal conductance models (SCMs). All SCMs after calibration were able to accurately match observations of sensible and latent heat flux, though the bias of the three SCMs with plant hydrodynamics (PHD) was slightly lower than that of two SCMs without PHD. Additionally, six idealized simulations were performed to study the impact of environmental variables on canopy processes. All SCMs agreed on the direction of simulated changes in canopy processes due to the changes in these environmental variables. ELM-MLCMv1 achieves a speedup of 25-50 times when comparing performance on a GPU relative to a CPU. This study provides the first necessary model development for including the representation of vertical canopies within ELM.