Measurements of jet substructure in Pb+Pb collisions provide key insights into the mechanism of jet quenching in the hot and dense QCD medium created in these collisions.This Letter presents a measurement of the suppression of large-radius jets with a radius parameter of R=1.0 and its dependence on the jet substructure. The measurement uses 1.72 nb−1 of Pb+Pb data and 255 pb−1 of pp data, both at sNN=5.02 TeV, recorded with the ATLAS detector at the Large Hadron Collider. Large-radius jets are reconstructed by reclustering R=0.2 calorimetric jets and are measured for transverse momentum above 200 GeV. Jet substructure is evaluated using charged-particle tracks, and the overall level of jet suppression is quantified using the jet nuclear modification factor (RAA). The jet RAA is measured as a function of jet pT, the charged kt splitting scale (d12), and the angular separation (ΔR12) of two leading sub-jets. The jet RAA gradually decreases with increasing d12, implying significantly stronger suppression of large-radius jets with larger kt splitting scale. The jet RAA gradually decreases for ΔR12 in the range 0.01−0.2 and then remains consistent with a constant for ΔR12 ≳ 0.2. The observed significant dependence of jet suppression on the jet substructure will provide new insights into its role in the quenching process.