This article addresses the optimal design of carbon-neutral hybrid energy system with deep water source cooling, biomass heating, and geothermal heat and power. A novel superstructure of the proposed hybrid energy system comprised of an enhanced geothermal system, a torrefied biomass-based combustion system, and a deep water source cooling system with conventional chillers as auxiliaries, is developed. Based on the superstructure of the proposed hybrid energy system, we develop a multi-period optimization model to minimize a fractional metric, the levelized cost. Because the main product of the hybrid energy system is heat, the levelized cost is expressed as levelized cost of heat, with other byproducts indirectly incorporated by using credits. The resulting nonconvex mixed-integer nonlinear fractional programming problem is efficiently solved by using a tailored optimization algorithm. Two case studies based on Cornell's campus in Ithaca, New York are presented to quantify the effect of different electric power sources on the technoeconomic objective, as well as the life cycle greenhouse gas emissions. The first case study considers electric power from natural gas, while a carbon-neutral electric power supply based on renewable geothermal energy is envisioned in the second case study. Results show that switching the electric power supply from natural gas to geothermal energy could reduce the greenhouse gas emissions by 24.5%, while only increasing the levelized cost of heat by 5.6%. The carbon footprint for both case studies are promisingly low, compared with numerous existing heat generation technologies. Through sensitivity analysis, the project lifetime is identified as the most influential input parameter.