Low-carbon energy application for both large grid and distributed energy consumers is an urgent problem to be solved. Data centers (DC) are the typical distributed large-size energy consumers, and the application of renewable energy and energy storage is a promising solution for data center decarbonization. This paper developed a complete hybrid energy system (HES) simulation process for data center applications. The photovoltaic (PV) cell, hydrogen electrolysis, hydrogen storage, proton exchange membrane fuel cell (PEMFC), lithium battery (BAT), grid, and data center load are considered in the HES. A one-dimensional two-phase flow PEMFC model is developed. The detailed mass transfer process inside the PEMFC cell is modeled. The PEMFC model-solving algorithm is developed and integrated into the HES simulation program. The energy management system (EMS) based on a logical flow chart energy management strategy is integrated by editable subfunction. The HES simulation program is coded and implemented based on the MATLAB-SIMULINK environment. The yearly HES performance simulations are conducted and analyzed for a 200 kW data center in Xi’an with different HES parameters and an appropriate HES parameter arrangement is provided. The main contribution of this work is the development of an editable HES simulation program that is extensible for data center applications.