Blockchain plays an important role in cryptocurrency markets and technology services. However, limitations on high latency and low scalability retard their adoptions and applications in classic designs. Reconstructed blockchain systems have been proposed to avoid the consumption of competitive transactions caused by linear sequenced blocks. These systems, instead, structure transactions/blocks in the form of Directed Acyclic Graph (DAG) and consequently re-build upper layer components including consensus, incentives, \textit{etc.} The promise of DAG-based blockchain systems is to enable fast confirmation (complete transactions within million seconds) and high scalability (attach transactions in parallel) without significantly compromising security. However, this field still lacks systematic work that summarises the DAG technique. To bridge the gap, this Systematization of Knowledge (SoK) provides a comprehensive analysis of DAG-based blockchain systems. Through deconstructing open-sourced systems and reviewing academic researches, we conclude the main components and featured properties of systems, and provide the approach to establish a DAG. With this in hand, we analyze the security and performance of several leading systems, followed by discussions and comparisons with concurrent (scaling blockchain) techniques. We further identify open challenges to highlight the potentiality of DAG-based solutions and indicate their promising directions for future research.