The invention discloses a forest tree breeding method and system based on a gene and protein regulatory network. The method comprises the following steps: positioning expression quantitative trait loci (eQTL), protein quantitative trait loci (pQTL) and metabolism quantitative trait loci (mQTL) according to the forming process of a phenotype, and forming a system model of the gene and protein regulatory network; positioning network quantitative trait loci (nQTL) influencing the gene and protein regulatory network according to the eQTL, the pQTL, the mQTL and the system model; generating a forest tree breeding application program according to the eQTL, the pQTL, the mQTL and the nQTL; conducting forest tree breeding according to the forest tree breeding application program. According to the forest tree breeding method based on the gene and protein regulatory network, the breeding period is greatly shortened, besides the target genes are consciously integrated according to the breeding target, the breeding direction is relatively precise, and the directional efficient breeding is realized.