Herein, we report a strong in-phase covariability of tropical cyclone (TC) activity between the Bay of Bengal (BOB) and the South China Sea (SCS) during October–December of 1979–2019, and which is also the dominant mode of BOB–SCS TC activity, accounting for 35% of the total variances in TC track density. This inter-basin TC covariance is closely linked to the anomalies of tropical sea surface temperature, appearing as the intrinsic Indo-Pacific Tripole mode, which significantly affects the atmospheric circulations overlying the BOB–SCS. Interestingly, this mechanism works via modulating the local TC genesis frequency in the BOB–SCS. However, in terms of the migrated TCs among them, the Indo-Pacific Tripole mainly regulates their genesis location but not their frequency. More importantly, such inter-basin TC covariability still exists significantly even when the TC track data migrating from the SCS into the BOB are excluded. After all, only 19 TCs during the 41 years (1979–2019) are observed to migrate from the SCS to the BOB, which can only contribute slightly to increasing the covariability of BOB–SCS TC-track activity, but do not play a dominant role. Further, the numerical simulations suggest that although both the Indian and Pacific Oceans contribute to the atmospheric anomalies that affect the BOB–SCS TC activity, the Pacific-effect is twice as important.