In Indonesia, especially in its intra urban areas or in between two urban areas, there are some problems of disparity, ineffective and inefficient mobility and degradation of environment. It becomes worst due to the decaying of its mass public transports. That is why this research will focus on improving public transports for two connected urban areas, Jakarta-Bandung. In its existing condition, there are several kinds of public transports, such as train, shuttle service, and private car. Each transport mode has a unique system and characteristic. Each passenger will choose their mode when it meets his or her criteria. In fact, the mode has not been chosen proportionally. There are a conflict between railway mode and toll way mode. The result is the decaying of train service. Thus the research has to concentrate more deeply in the development of railway transport. Moreover, this research will explore user characteristics and their preferences, and develop mode choice model with multinomial logit model. For advance research, we can use ISIL (Information System of Integrated Logistics). It is a concept that can provide an answer to this problem. The objective of ISIL is to contribute to integration at the conceptual level of all technical data related to a product throughout its life cycle. The concept used is the "Extended Enterprise". We give guidance for applying the concept ISIL in the field that interests us here.