Induced pluripotent stem cells (iPSCs) are derived from somatic cells that regain pluripotency by the nuclear programming with exogenous factors. iPSCs have immense potential applications in establishing disease models and understanding disease mechanisms, cell therapies, drug discoveries and assessments, etc. Over the past several years, scientists made much effort to improve reprogramming technology and achieved many breakthroughs in the research and applications of iPSCs. However, moving toward the eventual goal of clinical application, it is necessary to overcome challenges such as low reprogramming efficiency and risk due to tumorigenicity, besides the detailed mechanism of reprogramming remains to be elucidated. Here, combined with the recent advances in iPSCs, the progress of iPSCs were reviewed for research and applications. The current problems and the directions of future iPSCs research were discussed.