Adsorption using biochar is a high-efficient method for removing dyes from wastewater, and it has become a hot research topic in recent years. Biochar produced from organic wastes through pyrolysis is a promising way to combine bioenergy recovery and dye removal. In this study, durian shell (DS) was used as a feedstock for biochar and bio-oil production under different pyrolysis temperatures (400, 500, and 600 °C) for bioenergy recovery. Then, the biochar was applied as the absorbent for methylene blue (MB) removal from wastewater under batch and continuous experiments. It was found that the bio-oil production was slightly affected by temperature, while the productivity of biochar decreased from 42.05% to 30.65% with the increase in pyrolysis temperature from 400 to 600 °C. Compared with the biochar produced at 500 °C (DS-500) and 600 °C (DS-600), the biochar obtained at 400 °C (DS-400) exhibited higher MB removal efficiency and adsorption capacity under various pH conditions due to the superior microstructure. A high pH condition was beneficial for the adsorption process with DS-400. Additionally, the MB removal efficiencies increased with the increase in biochar dosage by providing more activated sites. A high MB content can promote the adsorption process, but a too high MB content negatively affects the removal efficiency due to the sorption saturation. Adsorption processes are more likely to match a pseudo-second-order model by chemical reactions. In the long-term continuous experiment, MB can be effectively removed to match the discharge standard by DS-400. This study provided a sustainable pathway for organic waste disposal and dye wastewater treatment.