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There has not been any certain recognition for the configuration of Kendeng Basin up to recent times. The thick quartered volcanic deposits at the top layer were one of the problems in imaging the configuration of this basin. Geological data interpret that the basement of Kendeng Basin has transitional properties between accretion and continental types. The pattern of a structure due to the collision between microcontinent Australia and Sundaland in this Basin are still questionable. The understanding of the structure pattern is essential due to it will control the formation of the Kendeng Basin. To adds the difficulty, the basement in this basin was not exposed to the surface. Geomagnetic methods were applied to analyze the configuration of the Kendeng Basin. The measurement of Geomagnetic has carried out in the Kendeng Basin in the West and Central Kendeng with the north-south relative line. The distance between measurement points is approximately 5 Km. The pattern of Kendeng Basin can be interpreted with data processing by apply regional-residual magnetic anomalies to obtain deeper anomalies. The structural analysis was carried out on regional Anomaly data by applying several derivative formulas to produce a pattern map of the Kendeng Basin. The results of this study indicate that the basement of the Kendeng basin is a block-faulting with the East-West relative direction. West-East trending structure is the main structure. We interpret the structure to have NE-SW oriented Meratus pattern which formed due to early-Eocene Collision.