The mainstream of development in knowledge discovery is researching on new high-performance and high-scalability mining algorithm. In fact, the research of process model and inner mechanism reflecting the law of knowledge discovery system or process and determining model and algorithm is more important, which has not got enough attention. This paper proposed a new independent knowledge discovery system framework, which combines those three elements: mechanism, model and algorithm. Through the cross-integration and comprehensive integration of several "systems framework", a kind of knowledge discovery theory based on inner cognitive mechanism(KDTICM) has been constructed. Researches and experimental results show that this high-starting point and high-level researches on the construction methodology are likely to form high-performance mining system methodology and new research direction; this researches on the KD(knowledge discovery) construction methodology can substantively involve domain knowledge long unresolved into "the solution to these important issues such as knowledge discovery process" and "dynamic real-time maintenance" of knowledge base; by exposing the essence, the regularity and complexity of KD would react on the mainstream development. Finally, the paper gave strong evidence of effectiveness of such construction methodology.