With the advent of flexible electronics, lithium-ion batteries have become a key component of high performance energy storage systems. Thus, considerable effort is made to keep up with the development of flexible lithium-ion batteries. To date, many researchers have studied newly designed batteries with flexibility, however, there are several significant challenges that need to be overcome, such as degradation of electrodes under external load, poor battery performance, and complicated cell preparation procedures. In addition, an in-depth understanding of the current challenges for flexible batteries is rarely addressed in a systematical and practical way. Herein, recent progress and current issues of flexible lithium-ion batteries in terms of battery materials and cell designs are reviewed. A critical overview of important issues and challenges for the practical application of flexible lithium-ion batteries is also provided. Finally, the strategies are discussed to overcome current limitations of the practical use of flexible lithium-based batteries, providing a direction for future research.