To construct the theoretical system of knowledge fusion in the big data era aims to provide basic theory and practical guidance for knowledge fusion in the big data era. According to the purpose and principle of the theoretical system of knowledge fusion in the era of big data, based on Lakatosian research programme, the theoretical system of knowledge fusion in the era of big data is constructed. The theoretical system of knowledge fusion in the era of big data is composed of basic theory of knowledge fusion, auxiliary hypothesis and application theory of knowledge fusion, and big data environment. Among them, the basic theory of knowledge fusion includes the concept and characteristics of knowledge fusion. The auxiliary hypothesis and application theory of knowledge fusion includes the thinking, supporting theory, demand, object, result, process, technology, method and tool of knowledge fusion. Inspired by the big data environment, the theoretical system of knowledge fusion can be expanded and modified continuously. The theoretical system of knowledge fusion in the era of big data solves the practical problems that the relevant theories of knowledge fusion are scattered and difficult to fully explain and guide the task of knowledge fusion in the environment of big data, and provides a reference for the theoretical research of knowledge fusion in the era of big data.