The task of finding all the minimal inconsistent subsets plays a vital role in many theoretical works especially in large knowledge bases and it has been proved to be a NP-complete problem. In this work, at first we propose a max-term counting based knowledge inconsistency checking strategy. And, then, we put forward an algorithm for finding all minimal inconsistent subsets, in which we establish a Boolean lattice to organize the subsets of the given knowledge base and use leaf pruning to optimize the algorithm efficiency. Comparative experiments and analysis also show the algorithm’s improvement over past approaches. Finally, we give an application for inconsistency measure calculation of fuzzy knowledge based systems.