Introduction: Chromosomal aberrations due to complex chromosomal rearrangements (CCRs) can cause abnormal phenotypes if accompanied by microdeletions or microduplications near the breakpoint, or gene breaks. Case Presentation: We report a prenatal diagnostic case of 2q14.3-q22.1 deletion with ultrasound suggestive of absent nasal bone accompanied by CCRs involving 6 chromosomes. Cytogenetic analysis revealed a karyotype of 46,XY,der(1)t(1;2)(p13.3;p11.2),der(2)t(1;2)inv(2)(q12q14.2)del(2)(q14.3q22.1),t(12;16)(q21.2;q12.1),t(13;21)(q32;q22.1). Chromosomal microarray analysis identified a 14.90 Mb deletion on 2q14.3q22.1. The copy number variant was de novo, as determined by karyotype analysis of the parents’ peripheral blood G-banding. Conclusion: The region contains haploinsufficient genes that can cause different phenotypes, mainly associated with neurodevelopmental and autism spectrum disorders. However, the genotype-phenotype correlation is limited in prenatal evaluation. Therefore, the combined use of multiple diagnostic techniques has an important role in the assessment of CCRs and genetic counseling.