A separation method and system for a byproduct 2M2BN in a course of producing 3PN by 2M3BN isomerization. The present invention proposes that in the course of producing 3PN by 2M3BN isomerization, a byproduct 2M2BN is produced, and 2M2BN will continuously accumulate in the system to suppress the isomerization reaction. The relative volatility of 2M2BN and 2M3BN is increased by using an extractant of the present invention, and separation of 2M2BN and 2M3BN and recycle of the extractant are completed in one distillation column with a partition plate, so that the equipment cost and difficulty are greatly reduced, and 2M2BN and 2M3BN products with high purity can be obtained.