The genetic antagonism between lean meat yield and meat quality dictates the need for precise selection in pigs. This study evaluated the impact of terminal sire lines (Duroc [D], Pietrain [P], and their F1 cross [PD]) on production traits and performed a genome-wide association study (GWAS) in a 1295 commercial population. Results revealed a clear genetic trade-off: D-sired progeny showed superior intramuscular fat (IMF) and meat color (p < 0.05), while P-sired progeny excelled in loin muscle area and leanness. PD-sired pigs generally showed intermediate performance and did not outperform the purebred terminal-sire groups for the major traits evaluated. GWAS replicated major known QTLs, including the VRTN locus for rib count (SSC7:97575068_A_G, p = 2.30e-39) and the BMP2 locus for carcass length (SSC17:15820953_G_A, p = 1.59e-09). Rib count was positively correlated with adjusted carcass straight length (r = 0.393, p = 5.80e-31), and combined genotype analysis of the VRTN and BMP2 loci revealed a joint effect on axial skeleton traits. Novel QTLs were discovered for drip loss (SSC13, SSC14) and myofiber perimeter (SSC1), with TUSC1 identified as a candidate gene. Our findings demonstrate that the PD cross does not mitigate the leanness-quality trade-off and highlight the VRTN and BMP2 loci, together with novel trait-associated markers, as potential targets for crossbred breeding programs.