Studies have analyzed U.S. tornado variability and correlated F1–F5 tornado occurrence with various natural climate oscillations and anthropogenic factors. Using a relatively new empirical mode decommission (EMD) method that extracts time-frequency modes adaptively without priori assumptions like traditional time-series analysis methods, this study decomposes U.S. tornado variability during 1954–2022 into intrinsic modes on specific temporal scales. Correlating the intrinsic mode functions (IMFs) of EMD with climate indices found that 1. the U.S. overall tornado count is negatively (positively) correlated with the Atlantic Multidecadal Oscillation (AMO) index (the Southern Oscillation Index (SOI)); 2. the negative (positive) correlation tends to be more prevalent in the western (eastern) U.S.; 3. the increase in weak (F1–F2) and decrease in strong (F3–F5) tornadoes after around 2000, when both the AMO and the Pacific Decadal Oscillation (PDO) shifted phases, are likely related to their secular trends and low-frequency IMFs; and 4. the emerging Dixie Tornado Alley coincides with an amplifying intrinsic mode of the SOI that correlates positively with the eastern U.S. and Dixie Alley tornadoes. The long-term persistence of these climate indices can offer potential guidance for future planning for tornado hazards.