The invention discloses a difference comparison method and system for graphical page programs. The method comprises the following steps: summarizing symbols of which output points are 0 and symbols of which all output connection points are not connected in pages, backtracking precursor symbols of the symbols in sequence according to a breadth-first traversing sequence to form call chains of the symbols, and summarizing the call chains to obtain a plurality of call chains of the pages; obtaining optimal matching of the call chains in two pages by adopting a connection relation similarity matching method; and matching the symbols in the matched call chains according to a quantity of call layers, symbol names and connection relations, performing alignment processing, inserting a plurality of blank nodes to form equal quantities of call chains, and comparing data and attributes such as symbol inputs, outputs and parameters in the call chains in sequence. The system comprises a hierarchical data management and loading module, a page difference analysis module, a graphical page display module, a call chain difference display module and a symbol difference display module.