Human Pangenome Reference Consortium (HPRC) and Chinese Pangenome Consortium (CPC) have pronounced the finish of the pilot work of the Human Pangenome Project, which aimed to build worldwide population-representative high-quality haplotype-resolved reference graph genomes. Graph-based gapless pangenome reference genomes with enriched genomic diversity and higher completeness and contiguity possessed the potential for a new beginning for third-generation sequencing (TGS)-based genomic research and high-performance mapping rate and variant genotyping for traditional short-read sequencing platforms. With the new pangenome reference coordinates and corresponding computation algorithms and methods, forensic integrative genomics fields will benefit in new-marker identification, highly-accurate marker genotyping, high-resolution panel development and corresponding statistical algorithm updates. Here, we discussed the past advances and new challenges of pangenome-based genomic research and their integrative genomics applications for variant identification and new forensic genomic, epigenetic, transcriptomic, and microbiome practices. We highlighted the necessity and importance of including the forensic TGS-based platforms, pangenome-based entire landscape of genomic diversity, pangenome-based study design and graph-based pangenome reference in short-read NGS mapping and TGS-based innovations to achieve forensic precision medicine.