Stationary intensive observations over the Indian Ocean (0°, 80.5°E) with the research vessel Mirai were conducted using shipborne lower troposphere radar (SB-LTR) on the Mirai Indian Ocean Cruise for the Study of the MJO-convection Onset field experiment from 28 October to 20 November 2006. Sea surface temperature (SST) showed large diurnal variations when there was little cloud cover, and large specific humidity was confirmed around the surface of the sea. A few days later, when small cloud clusters passed over Mirai, strong updrafts were observed by SB-LTR up to 1.5 km altitude above the level of free convection (LFC), the mixing layer observed by SB-LTR showed large diurnal variations, and specific humidity decreased around the surface of the sea. These results suggested that local convective instability related to large diurnal variations of SST caused large diurnal variations of the mixing layer and strong updrafts and contributed to developing cloud clusters. Super cloud clusters related to the Madden-Julian Oscillations (MJO) proceeded eastward over Mirai between 16 and 20 November. At the same time, horizontal winds showed a large-scale convergence, specific humidity, and the equivalent black body temperature (T_BB) showed similar time-height variations. A strong mixing layer and updrafts were also observed up to an altitude of 1.5 km using SB-LTR, which were also above the LFC; however, large diurnal variations of the mixing layer were not confirmed. Specific humidity was relatively large around the surface of the sea, which was quite different from the results in the small cloud clusters. These results indicated that the small cloud clusters could be caused by local convective instability, but MJO convections would be correlated by large-scale convergence.