Embodiments of methods and systems for quality of service (QoS)-aware input/output (IO) management for a Peripheral Component Interconnect Express (PCIe) storage system with reconfigurable multi-ports are described. In an embodiment, a method includes receiving, in a receiver interface, an IO request from a software application, the IO request comprising information for communicating data over a data access port. The method may also include determining, in a transfer mode selector, a transfer mode selection for communicating the data over the data access port, the transfer mode being selected from a throughput-oriented mode, a latency-sensitive mode, or a balanced mode. Additionally, the method may include communicating, by a block distribution unit, the data over the data access port in response to the IO request, and according to the data transfer mode.