This study examined the effects of immunocastration and surgical castration on the histomorphometric and transcriptome traits of the porcine skeletal muscle. We hypothesized that the differences in duration of androgen deprivation resulting from different castration methods influence skeletal muscle biology in a muscle-specific manner. This was tested by analyzing samples of m. longissimus dorsi (LD) and m. semispinalis capitis (SSC) from immunocastrated (IC; n = 12), entire male (EM; n = 12), and surgically castrated (SC; n = 12) pigs using enzyme/immunohistochemical classification and histomorphometric analysis of myofibers, quantitative PCR, and RNA sequencing. The results confirmed the distinctive histomorphometric profiles of LD and SSC and the castration method related muscle-specific effects at the histomorphometric and transcriptome levels. Long-term androgen deficiency (surgical castration) significantly reduced the proportion of fast-twitch type IIa myofibers in LD (P<0.05), whereas short-term androgen deprivation (immunocastration) reduced the cross-sectional area of oxidative type I myofibers in SSC (P<0.05). At the transcriptional level, glycolytic LD adapted to long- and short-term androgen deprivation by upregulating genes controlling myoblast proliferation and differentiation to maintain fiber size. In contrast, increased protein degradation through the ubiquitin ligase-mediated atrophy pathway (significantly increased TRIM63 and FBXO32 expression; P<0.05) could underly reduced cross-sectional area of type I myofibers in the oxidative SSC in IC. Potential candidate genes (HK2, ARID5B, SERPINE1, and SCD) linked to specific metabolic profiles and meat quality traits were also identified in IC, providing a foundation for studying the effects of immunocastration on skeletal muscle fiber and carcass/meat quality traits.