The dried flower buds of Magnolia biondii Pamp are one of the most widely used medicinal plants officially listed in the Chinese Pharmacopoeia. A 2-D column-switching system without sample loop trapping, where two columns were switched directly via a six-port two-position switching valve, was successfully applied for the first time to the isolation and purification of five lignans including pinoresinol dimethyl ether, magnolin, epi-magnolin A, fargesin, and demethoxyaschantin from M. biondii Pamp after microwave-assisted extraction. The introduction of the six-port switching valve instead of sample loop assured 100% recovery from the first dimension to the second, and the injection volumes of the second dimension could reach 12 mL. In this mode of operation, the solvent consumption of the 2-D approach was less than 30% that of conventional gradient methods with even larger sample size. The simultaneous operations of the two dimensions allowed the cycle time to be less than 16 min, compared to 90 min in the gradient elution single-dimension mode of operation. All of the five lignans were isolated at high purities of over 99% with approximately 95% recoveries.