Beginning in the 21st century, e-business enterprises need to take vigorous tactics in facing greater challenges in a booming cyber commerce era. In today’s e-business environment, innovative interface technologies change with each passing day, customers’ (users’) satisfaction are more and more discerning, and market demands can fluctuate unpredictably. While facing constant changes in the lower-profit and high customer-service cyber commerce environment, it is important to know how to break through the current Information Technology (IT) industrial situation, maintain the enterprises’ owned advantage and continuously make a profit under a booming transition. In this research, nineteen sub-criteria are categorized into five factors (criteria) by the measurement of factor analysis. Three basic types of innovative business websites (portals, cyber commerce and social community) in an e-business environment are then evaluated by nineteen assessable criteria of five characteristics of innovation interface technology through the use of the Analytical Network Process (ANP) approach. The specific feature of the ANP model is to establish a pairwise comparative matrix and furthermore, to calculate the priority vector weights (eigenvector) of each assessable characteristic, criteria and sub-criteria. The factor analysis can utilize more measure matrix to benefit the deviation of ANP approach due to less data from expert’s opinions. Additionally, in the content, the analytical hierarchical relations are definitely expressed in four levels among each characteristic of innovative interface technology (IIT), criterion and sub-criteria. Moreover, based on the empirical analysis, the enterprises are able to choose the best potential business website with highest economic value added (EVA) through this research in order to maximize financial profits and benefits from an innovative perspective. Finally, some suggestions for managers and researchers are inductively formed to further determine the best development of innovative interface technologies in a thriving cyber commerce environment.