The propagation of intraseasonal Kelvin waves in the Indonesian seas significantly modulates the Indonesian Throughflow (ITF) transport. However, their northward propagation across the equator within the main ITF route, particularly through the Makassar Strait, has remained unverified due to a lack of in situ observations. This study presents simultaneous mooring observations of current velocity profiles at the choke points in the ITF's main pathway, from the Lombok Strait to the northern Makassar Strait. Our results confirm the propagation of intraseasonal Kelvin waves cross the equator reaching the northern Makassar Strait, primarily along the 100-m isobath. During the propagation, the dominant modes are the first and second baroclinic modes in the Indian Ocean, the second and third baroclinic modes between the Lombok and southern Makassar Straits, and the third to fifth baroclinic modes between the southern and northern Makassar Straits. Vertical mode decomposition reveals that the intraseasonal velocity anomaly in the northern Makassar Strait comprises the first five baroclinic modes, with the first two modes dominant in the upper 400 m and the third to fifth modes dominant at depths of 400–800 m. The cross-equator propagation of Kelvin waves through the Makassar Strait plays a pivotal role in linking oceanic fluctuations between the Pacific and Indian Oceans.