The longstanding goals of storage system design have been to provide simple abstractions for applications to efficiently access data while ensuring the data durability and security on a hardware device. The traditional storage system, which was designed for slow hard disk drive with little parallelism, does not fit for the new storage technologies such as the faster flash memory with high internal parallelism. The gap between the storage system software and flash device causes both resource inefficiency and sub-optimal performance. This dissertation focuses on the rethinking of the storage system design for flash memory with a holistic approach from the system level to the device level and revisits several critical aspects of the storage sy...