It is disclosed a method and system based on machine learning for reconstructing biological wastewater treatment processes; the method includes: acquiring influent and effluent basic quality, ecological risk and process information data on the biological wastewater treatment process, and performing data preprocessing; performing feature extraction and multi-unit characterization on the biological wastewater treatment process; constructing effluent basic quality prediction models and effluent ecological risk prediction models of different biological treatment multi-unit combination processes, and performing standard-reaching validation; simulating and reconstructing different biological wastewater treatment short-range unit combination processes, and performing effluent quality standard-reaching validation under different influent quality scenarios; and evaluating ecological risk of the reconstructed short-range biological treatment unit combination processes with the effluent quality up to standard, and determining the optimal biological wastewater treatment process.