Urban pattern is the result of a dynamic transformation process, which can follow two different trajectories: planned interventions generally produces clear geometrical patterns in large areas, however, unplanned transformation process needs more time and has relatively smaller and partial effects on the urban pattern but creates more complex urban patterns. Highly complex spatial structure of urban pattern governed by local and global forces should be analyzed via advanced methods that corresponds the complexity of the pattern. Analyses of the dynamic structure of the multidimensional urban system shows the necessity of using advanced methods and several parameters together. The aim of this paper is developing a new method to analyze and represent highly complex urban pattern via evaluating geometrical, topological, and mathematical parameters to evaluate essential characteristics of cities. Physical space is analyzed by ‘geometrical parameters’, ‘topological parameters’, ‘parameters related to use and perception’ and ‘parameters related to complexity’. Calculation results gives two main information about urban structure: Firstly, values gives information about spatial characteristics and diversity of urban pattern. Secondly, the spatial distribution map of changing urban pattern reflects the unique structure of settlements, which resembles DNA of living creatures. In this paper, Istanbul was selected as case study area because of the rich historical background and dynamic urban growth process resulting various types of settlements including historical settlements, old villages, unplanned development, squatter areas and gated communities with different densities. As the proposed model shows essential morphological characteristics of urban pattern as a morphological DNA, outputs of this model has a potential to be used in different areas such as comparative analysis of geometrically different cities, analyzing irregularities in urban pattern, controlling growth and density by controlling parameter values, creating urban sub-systems by combining components in different scales.