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In the Makassar Strait, upwelling occurred by wind-driven current and complexity of bottom topography. Analysis of upwelling phenomena could be determined by salinity, temperature dan three-dimensional current value which happened on a year as a climatology change. Regional Ocean Modelling System (ROMS) is a terrain following three-dimensional model to calculate numerical value which need stability for long-duration simulation. The model has been simulated for 1 years from 1 January 2017 to 31 December 2017 and verified by tidal data. Horizontal Boundary Condition which contain u-v velocities, salinity and temperature, is a climatology data from GLBa0.08 HYCOM. While Vertical Boundary used as atmospheric forcing is a data from ERA-INTERIM ECMWF. The verification use RMSE and RRE methods, showed good result between model and observation data with RMSE=0.1454 meter, and RRE=6.5806%. The result was analysed from 12 sampling points, 6 points on the outflow of the Makassar Strait which generated upwelling and the 6 others on the canal that connect to the Flores Sea and Java Sea. Model giving good result on January, indicate average w-velocity is 9.1183 m/day