Marine macroalgae (seaweed) is a promising feedstock for producing biohydrogen and biomethane via dark fermentation and anaerobic digestion, respectively. However, one of the limiting steps in the biological process is the conversion of polymeric carbohydrates into monomeric sugars. Here hydrothermal pretreatments were assessed for hydrolysis and subsequent production of biohydrogen and biomethane from the brown seaweed Saccharina latissima. The solubilization of S. latissima improved with increasing temperatures from 100 to 180 °C, resulting in a maximum yield of 0.70 g soluble chemical oxygen demand/gram volatile solid (sCOD/g VS); equivalent to an increase of 207.5% compared with untreated seaweed. However, the yield of the derived monomeric sugar mannitol peaked at 140 °C and decreased with increasing temperatures, likely due to production of fermentative inhibitors. Microstructural characterization revealed that the algal structure was significantly damaged, and the major chemical groups of carbohydrates and proteins were weakened after pretreatment. Regardless of hydrothermal temperatures, biohydrogen yield only slightly increased in dark fermentation, while biomethane yield significantly increased from 281.4 (untreated S. latissima) to 345.1 mL/g VS (treated at 140 °C), leading to the sCOD removal efficiency of 86.1%. The maximum energy conversion efficiency of 72.8% was achieved after two-stage biohydrogen and biomethane co-production. In comparison, considering the energy input for pretreatment/fermentation/digestion, the highest process energy efficiency dropped to 37.8%. Further calculations suggest that a significant improvement of efficiency up to 56.9% can be achieved if the heat from pretreatment can be recovered.