In recent years, applying ecological concepts into landscape designs to enhance biodiversity within urban areas has become an important strategy worldwide. A commonly adopted strategy for the development of systems is to estimate the ecological effectiveness of relative landscape mosaics. Biotope Area Factor (BAF) is a general methodology that is used, however it only considers the land use surface types of the landscape mosaic unit using aerial photos and expert questionnaire method. It is not clear whether the ecological effectiveness of areas estimated by BAF system is congruent with the actual ecological characteristics and diversity of inhabiting organisms. The practicality of the BAF systems are evaluated in this study by comparing the BAF values of homogenous units amongst eight urban university campuses in central Taiwan with vegetation density/structure and arthropod/plant diversity collected in situ. We used linear models to evaluate the relationship between BAF values and in situ arthropod/plant diversities and vegetation structures. The results showed that BAF values of various homogenous units were partially correlated with vegetation structure, but were incongruent with in situ diversity of plants and arthropod. Our findings indicated that the current urban area ecological effectiveness quantifying BAF system may not be appropriate. For future studies, we suggest that the operation scale should be adjusted and factors influencing biodiversity should be considered in the weighting system to realistically and precisely designate the ecological effectiveness of landscape mosaic units.