The inter-annual variability of boreal summer intra-seasonal oscillation (BSISO) propagation from the Indian Ocean (IO) to the western Pacific (WP) is investigated for the boreal summers (May to September) of 1979–2018. It is shown that the interannual variability of BSISO mainly happens in its evolution, not in its strength over the IO. Here, we classify four distinctive modes for inter-annual variability of BSISO propagation: (i) northeast mode, propagating from the IO to the western equatorial Pacific (WEP) and the western North Pacific (WNP); (ii) north-only mode, only propagating to the WNP; (iii) east-only mode, only propagating to the WEP; and (iv) stationary mode, propagating to neither the WEP nor the WNP. It is found that the Maritime Continent (MC) and WEP are two key regions determining these four modes concerning mean state moisture and vertical motion. Associated with central equatorial Pacific cooling, the BSISO of northeast and north-only modes can reach the WP by passing over the MC due to positive mean moisture anomalies and upward mean motion anomalies over the MC. The strong negative mean moisture anomalies and downward mean motion anomalies over the WEP, related to strong central Pacific cooling, prevents the development of BSISO there, resulting in north-only mode. For the east-only and stationary modes associated with the central Pacific warming, their BSISO can hardly pass the MC due to negative mean moisture anomalies and downward mean motion anomalies. The positive mean moisture anomalies and upward mean motion anomalies over the WEP related to strong central Pacific warming, however, will reinitiate the BSISO in the WEP for the east-only mode.