Aphid infestation constrains goji berry production, yet its defense architecture remains poorly resolved. We integrated comparative transcriptomics, phytohormone profiling, small RNA sequencing, and genome-wide nucleotide-binding leucine-rich repeat (NLR) analysis to dissect aphid defense in Lycium barbarum (cv. Ningqi-10)and susceptible L. chinense. Aphid bioassays confirmed that L. barbarum imposes a significant fitness cost on aphids, reducing survival, longevity, and fecundity. Transcriptomic comparison revealed fewer but more defense-enriched differentially expressed genes in the resistant accession. Weighted gene co-expression network analysis (WGCNA) identified a stress-associated turquoise module (288 genes, r = 0.981) receptor-like kinases and mitogen-activated protein kinase (MAPK) components, bridging extracellular signals sensing and hormone signaling. Phytohormone profiling showed that salicylic acid (SA) accumulated to 72 h, whereas jasmonic acid (JA) peaked transiently at 24 h, producing an increased SA/JA ratio suggesting a shift to SA-dominated signaling. MiR398a-3p and miR319-3p dynamics coincided with this SA/JA shift, suggesting a possible link to hormone-coordinated regulation and candidate targets for validation. NLR analysis identified 151 candidate genes, including 18 L. barbarum-biased NLRs up-regulation under SA-dominated signaling, implying a link to SA signaling. Collectively, these findings support a multi-layered framework integrating SA signaling, transcriptional reprogramming, and coupled miRNA and NLR responses in aphid defense.