The TNNC2 gene encodes the fast-skeletal C subunit of the troponin complex that plays a vital role in the regulation of striated muscle contraction and could be a candidate gene for pork quality. Here, we identified coupled insertion/deletion (indel) variants, a 17-bp insertion and an 11-bp deletion, in porcine TNNC2. The coupled indel variants provide an alternative splicing donor site and cause a 42-bp truncation in the first exon of TNNC2-201, leading to increased expression of TNNC2-201. Polymorphism of the two indel variants is associated with the average backfat thickness (p = 3.16 × 10-3 ), pH value 24 h post-slaughter (p = 4.31 × 10-4 ), intramuscular fat (IMF) content (p = 1.54 × 10-2 ), and myofiber cross-sectional area (p = 2.86 × 10-2 ) of longissimus dorsi in a population of 425 Duroc (♂) × Luchuan (♀) pigs. In an independent population of 1,304 commercial hybrid pigs, we further confirmed that it is associated with the IMF content (p = 1.75 × 10-4 ), pH value 45 min post-slaughter (p = 6.34 × 10-3 ), and drip loss (p = 2.88 × 10-2 ) of the longissimus dorsi muscle. An increased frequency of the mutant allele is linked to increased IMF content, smaller myofibers, and a relatively moderate pH value. Furthermore, we detected a mutant allele frequency of 96.67% in Luchuan pigs and 86.67% in Tongcheng pigs, whereas the frequency was 0.91% in Duroc pigs, 2.04% in Landrace pigs, and 0% in Yorkshire and Pietrain pigs, indicating its opposing distributions in lean-type and Chinese local pig breeds. The present results establish coupled indel variants of TNNC2 as a novel molecular marker for meat quality improvement.