Genomic structural variation is generally defined as deletions, insertions, duplications, inversions, translocations or copy number variation (CNV) in large DNA segments (>1 kb). The structural variation in an individual genome includes thousands of discrete regions, spans millions of base pairs, and encompasses numerous entire genes and their regulatory regions. This results in missing or change of gene functions, and subsequently leads to phenotypic changes, disease susceptibilities or induction of diseases. Research on genomic structural variation is useful in analyzing the integrated genotype with genomic variation and understanding the potential medical effects and the entire function of the organism. Here, we reviewed the latest research progresses of the types of human genomic structural variants and the methods for disclosing these variants, as well as the impact of the variants on individual phenotype, disease, and evolution.