With the advent of big data and the information age, the data magnitude of various complex networks is growing rapidly. Many real-life situations cannot be portrayed by ordinary networks, while hypergraphs have the ability to describe and characterize higher order relationships, which have attracted extensive attention from academia and industry in recent years. Firstly, this paper described the development process, the application areas, and the existing review research of hypergraphs; secondly, introduced the theory of hypergraphs briefly; then, compared the learning methods of ordinary graphs and hypergraphs from three aspects: matrix decomposition, random walk, and deep learning; next, introduced the structural optimization of hypergraphs from three perspectives: dynamic hypergraphs, hyperedge weight optimization, and multimodal hypergraph generation; after that, the applicability of three uncertain hypergraph models were analyzed based on three uncertainty theories: probability theory, fuzzy set, and rough set; finally, the future research directions of hypergraphs and uncertain hypergraphs were prospected.