The lengths of a pig's small intestine length (SIL) and cecum-colon length (C-CIL) are crucial for nutrient absorption and substantially affect feed utilization efficiency. Thus, selecting for increased intestinal lengths could enhance feed digestibility. However, conventional methods for measuring these traits pose considerable challenges. To address these drawbacks, we explored the use of molecular breeding techniques to refine the selection process. In this study, 413 age-matched Yorkshire barrows were humanely killed, and their SIL and C-CIL were measured. Genotyping was conducted using a 50K single nucleotide polymorphism (SNP) array, and the SNP-chip data were imputed to whole-genome sequencing data (iWGS). The heritability estimates for SIL and C-CIL were 0.25 and 0.26, respectively. Utilizing genome-wide association studies based on chip and iWGS data, significant SNPs on Sus scrofa chromosomes (SSC) 2 and SSC9 for SIL traits and SSC16 for C-CIL traits were identified. Specifically, two novel quantitative trait loci (QTLs) regulating SIL on SSC2 and SSC9 were identified. Furthermore, one novel QTL regulating C-CIL on SSC16 was identified. Bayes fine mapping narrowed the confidence intervals for these QTLs to 1.91 Mb (from 42.37 to 44.28 Mb on SSC2) and 1.92 Mb (from 43.96 to 45.92 Mb on SSC9) for SIL and 1.96 Mb (from 11.14 to 13.10 Mb on SSC16) for C-CIL. Based on the biological functions of genes, SRY-box transcription factor 6 on SSC2 and apolipoprotein A4, SID1 transmembrane family member 2, transgelin, and transmembrane serine protease 13 on SSC9 were identified as novel candidate genes for SIL. Likewise, cadherin 10 on SSC16 was identified as the novel candidate gene for C-CIL. Overall, these findings offer insights into identifying the causal genes and mutations affecting SIL and C-CIL. Additionally, they highlight novel molecular markers that can be utilized for the molecular breeding of intestine traits in Yorkshire pigs.