The invention relates to a seedling culture method of zanthoxylum armatum var.novemfolius. The seedling culture method specifically comprises the following steps of (1) selecting 10 parts of garden soil by weight, 5 parts of peat by weight, 1 part of grain husk by weight and 2 parts of cattle barnyard manure by weight, uniformly mixing, adjusting the pH (potential of hydrogen) value to 7, and fermenting for 10 to 15 d, so as to obtain a culture medium; (2) soaking the seeds of the zanthoxylum armatum var.novemfolius by a detergent powder solution with concentration of 1 wt% for 4 h, repeatedlyrubbing the seeds until the grease on the husks of the seeds of the zanthoxylum armatum var.novemfolius is removed, cleaning by clean water, and coating by plant ash, so as to obtain the seeds of thezanthoxylum armatum var.novemfolius; (3) loading the culture medium obtained in step (1) into a nonwoven fabric bag, so as to obtain a seedling culture bag; (4) putting the seeds of the zanthoxylum armatum var.novemfolius obtained in step (2) into the seedling culture bag, spraying water until the culture medium is wet, and covering the seedling culture bag with the culture medium with a thickness of 3 to 5 cm, wherein each seedling culture bag is loaded with one seed of the zanthoxylum armatum var.novemfolius; (5) irrigating the seedling culture bag with the fertilizer and water after seeding, and removing the diseases and pests; after the seedlings of the zanthoxylum armatum var.novemfolius grow to 30 cm, directly transplanting the seedlings.