Microalgae are rich in carotenoids, vitamins, proteins, polyunsaturated fatty acids and other nutrients required by humans and animals. In addition, some microalgae also play critical roles in aquatic ecological environment. Thus, it is important to carry out microalgal research for practical applications. Traditionally, analysis of microalgal components requires cell disruption and extraction with organic solvents followed by gas or liquid chromatography of the extracts. However, these traditional methods are generally time-consuming, requiring expensive instruments and sophisticated operations. So it is urgent to develop a more effective method for rapid and convenient microalgal analysis. Infrared spectroscopy mainly relies on the absorbance of radiation at molecular vibrational frequencies to observe the changes of the molecular compositions, characteristics, structures and concentrations. Actually, this technique has emerged as a promising tool to distinguish and quantify various cellular components such as proteins, lipids, nucleic acids, carbohydrates, chlorophyll and carotenoids in microalgal systems. Compared with the conventional detection methods, it has the advantages of simple, fast, non-invasive, and multiplex measurements. Especially, with the development of microscopic imaging technology, infrared microspectroscopy shows the powerful potential for spatially-resolved and real-time in situ measurements of biological systems at the single cell or tissue level. In recent years, with the development of synchrotron radiation technique, the advanced synchrotron infrared microspectroscopy and imaging technique has been applied and it can provide higher sensitivity and spatial resolution than the traditional infrared spectroscopy, so to a certain degree it resolves the contradiction between high throughput analysis and high spatial resolution observation. In this study, the principle and advantages of infrared spectroscopy and micro-spectroscopic imaging were firstly illustrated, especially the application of this technique combined with chemometrics in the field of biology. Then, the recent progress on the application of infrared spectroscopy in discrimination, metabolism, breeding, water environment protection, medicine and health relating to microalgal research was introduced and discussed in review of a variety of recent literature. For instance, infrared spectroscopy in combination with chemometrics can identify, discriminate or classify different microalgal strains. This technique can also be applied in the research of microalgal growth and metabolism based on its advantages of fast and multicomponent analysis. It can even provide a non-destructive and high-throughput method to screen the lipids, β-carotene or astaxanthin hyperproducing microalgal strains based on infrared spectroscopic tool. In addition, microalgae have been reported to be potentially proper biosorbents for the treatment of heavy metals and dyes wastewater. Actually, infrared spectroscopy has already been applied as a proper approach to study biosorption of heavy metals or dyes from wastewaters using microalgae. Being a powerful tool, it has not only distinguished and quantified various vital components quickly and conveniently, but has also provided an effective method for quality detection and authenticity measurement of microalgal foods and drugs. Although there are still some deficiencies for the application of infrared spectroscopy in microalgal research, the promising potential and comprehensive resolution for it are discussed in this study. Finally, based on the latest progress and application of infrared spectroscopy, some prospects of this technique for microalgal research were also put forward at the end of the review, such as industrial large-scale culture of microalgae, selection and breeding of hyperproducing strains, the physiology of microalgae, the molecular structure and function of organelles, etc.