The refining industry is shifting from decarbonization to hydrogenation for processing heavy fractions to reduce pollution and improve efficiency. However, the carbon footprint of hydrogen production presents significant environmental challenges. This study couples refinery linear programming models with life cycle assessment to evaluate, from a long-term perspective, the role of low-carbon hydrogen in promoting sustainable and profitable hydrogenation refining practices. Eight hydrogen-production pathways were examined, including those based on fossil fuels and renewable energy, providing hydrogen for three representative refineries adopting hydrogenation, decarbonization, and co-processing routes. Learning curves were used to predict future hydrogen cost trends. Currently, hydrogenation refineries using fossil fuels benefit from significant cost advantages in hydrogen production, demonstrating optimal economic performance. However, in the long term, with increasing carbon taxes, hydrogenation routes will be affected by the high carbon emissions associated with fossil-based hydrogen, losing economic advantages compared to decarbonization pathways. With increasing installed capacity and technological advancements, low-carbon hydrogen is anticipated to reach cost parity with fossil-based hydrogen before 2060. Coupling renewable hydrogen is expected to yield the most significant economic advantages for hydrogenation refineries in the long term. Renewable hydrogen drives the transition of refining processing routes from a decarbonization-oriented approach to a hydrogenation-oriented paradigm, resulting in cleaner refining processes and enhanced competitiveness under emission-reduction pressures.