Recently, various types of structural systems for skyscrapers are studied as the height and size of the building structures rapidly increase due to social and economical needs. The mega frame system among them, which is the structural system developed recently, is known as a suitable structural system for skyscrapers because this structural system has sufficient stiffness against the lateral forces by combination of mega members which consist of many columns and girders. Since the mega frame structure has significant numbers of elements and nodes, it takes tremendous times and computer memories to analyze and design the structures. Therefore, the exclusive structural analysis program for mega frame system is developed to reduce the efforts and time required for the analysis and design of mega frame structure. To this end, an efficient modelling technique using the characteristics of mega frame structures and an efficient analytical model, which uses a few DOFs selected by the user using the matrix condensation method, are developed in this study. Static and dynamic analyses are conducted using an example structure. The effectiveness and accuracy of the developed program we verified by the comparison between the results of the proposed method and the conventional method.