The thermal conductivity (λ) of carbon nanotubes (CNTs) with chirality indices (5,0), (10,0), (5,5), and (10,10) has been studied by reverse nonequilibrium molecular dynamics (RNEMD) simulations as a function of different bond length alternation patterns (Δr(i) ). The Δr(i) dependence of the bond force constant (k(rx) ) in the molecular dynamics force field has been modeled with the help of an electronic band structure approach. These calculations show that the Δr(i) dependence of k(rx) in tubes with not too small a diameter can be mapped by a simple linear bond length-bond order correlation. A bond length alternation with an overall reduction in the length of the nanotube causes an enhancement of λ, whereas an alternation scheme leading to an elongation of the tube is coupled to a decrease of the thermal conductivity. This effect is more pronounced in carbon nanotubes with larger diameters. The formation of a polyene-like structure in the direction of the longitudinal axis has a negligible influence on λ. A comparative analysis of the RNEMD and crystal orbital results indicates that Δr(i) -dependent modifications of λ and the electrical conductivity are uncorrelated. This behavior is in-line with a heat transfer that is not carried by electrons. Modifications of λ as a function of the bond alternation in the (10,10) nanotube are explained with the help of power spectra, which provide access to the density of vibrational states. We have suggested longitudinal low-energy modes in the spectra that might be responsible for the Δr(i) dependence of λ.