Underutilized horticulture crops have not been fully utilized in terms of their potential contributions to food security, income generation, and environmental sustainability. In recent years, various omics technologies such as genomics, metagenomics, transcriptomics, proteomics, metabolomics, phenomics, and ionomics have emerged as valuable tools for studying the genetic and molecular basis of these underutilized crops. The use of high throughput technologies like next-generation sequencing (NGS) has allowed for the rapid generation of omics data, which can be used to explore the genetic resources of underutilized horticultural crops. The advancement of sequencing technology and bioinformatics tools has greatly facilitated molecular biology studies of these crops. By integrating multiple omics approaches, researchers can gain insights into gene functions and networks under conditions of physiological and environmental stress. An innovative and proactive approach to preserving underutilized fruit plants through the application of biotechnological methods including in vitro culture technology, cryopreservation, and molecular markers. This article provides an overview of the current and potential use of various omics approaches in exploring information about important underutilized horticulture crops, with the aim of promoting basic research and accelerating the development of new varieties.