Abstract: As the largest and deepest Cenozoic rift basin in Indonesia, the Kutei Basin is one of the most favorable basins for hydrocarbon exploration. The major exploration targets and intervals in the basin are mainly concentrated so far in the Middle to Upper Miocene deltaic systems, and the deeper intervals below the Middle Miocene have not been fully explored yet. Drilling and field investigation suggest that the Lower Miocene is composed of shallow marine depositional systems. From the bottom to the top, it changes from dark shale, progradational sandstone to bioclastic limestone. which marks the top of the shallow marine sequence. The bioclastic limestone covered the sandstone, and buried by thick shales, showing obvious features of mixed siliciclastic – carbonate deposition. Such a mixed deposit represents a sequence formed in a specific environment with relatively high sea level in the beginning, followed by sea level falling, and sea level rise again. The shale sediments were deposited during the period of highest sea level; while the sandstone was deposited during sea level falling stage. Then the sea level rise made the environment favorable for bioclastic to grow up. Bioclastic would stop develop when the sea level was rising too fast and the water became too deep. Above the bioclastic mudstone deposited. The frequent sea level fluctuation will cause the formation of multiple interbedded siliciclastic - carbonate sequences. This model reveals that under the compressive stress, the tectonic movements was frequent and active in this region. Relative sea level changed rapidly, that caused the deposition of the cyclic mixed deposits.