For the low carbon hybrid flow shop scheduling problem(HFSP), a novel shuffled frog-leaping algorithm (SFLA) is proposed to minimize simultaneously total energy consumption and total tardiness. Some worst solutions of population are excluded out of memeplexes. New solutions are generated by using new strategies for memeplex construction and memeplex search. Optimization data of search process are utilized to substitute for the worst solutions out of memeplexes and update archive to improve solution quality. A series of examples are given to demonstrate the effectiveness of the new SFLA. The analysis of computational results show that the new SFLA has strong search ability and advantages in solving the low carbon HFSP.