Seasonal variations are significant in currents in the Makassar Strait, 80% of the Indonesian Throughflow (ITF) from the Pacific to the Indian Ocean, and they are in phase with both the monsoon and the sea surface height anomaly (SSHA) difference between two oceans. However, dynamics are not well discussed since gridded SSHA products within the strait are less reliable because of both over-smoothing and contamination in coastal areas. In this study, therefore, 17 years of along-track Jason altimetry data with the ALES retracker are used without grid interpolation to investigate seasonal SSHA variations in and around the Makassar Strait. All SSHA variations are in phase from the southern Celebes Sea to the northern Java Sea through the Makassar Strait, but their amplitude decreases by the distance from the southern shallow area. These amplitude modulations produce the pressure gradient force, which is maximum to the north of 4°S reaching 1.5 × 10⁻⁶ ms⁻², and that would be balanced with the bottom friction of the upper-layer ITF velocity, rather than the wind stress whose magnitude 5 × 10⁻⁸ ms⁻² is too small. The SSHA difference between the two oceans is in phase but is isolated from the Makassar Strait by adjacent uncorrelated SSHA variations.