Most deep energy renovation projects focus only on an operating energy reduction and disregard the added embodied energy derived from adding insulation, window/door replacement, and mechanical system replacement or upgrades. It is important to study and address the balance and trade-offs between reduced operating energy and added embodied energy from a whole life cycle perspective to reduce the overall building carbon footprint. However, the added embodied energy and related environmental impact have not been studied extensively. In response to this need, this paper proposes a holistic sustainability index that balances the trade-off between reduced operating energy and added embodied energy. Eight case projects are used to validate the proposed method and calculation. The findings demonstrate that using a balanced sustainability index can reveal results different from a conventional operating energy-centric approach: (a) operating energy savings can be offset by the embodied energy gain, (b) the operating energy savings do not always result in a life cycle emissions reduction, and (c) the sustainability index can vary depending on the priorities the decision makers give to operating carbon, embodied carbon, and operating cost. Overall, the proposed sustainability score can provide us with a more comprehensive understanding of how sustainable the renovation works are from a life cycle carbon emissions perspective, providing a more robust estimation of global warming potential related to building renovation.