In this article, the problem of semi-parametric inference on the parameters of a multidimensional Lévy process $L_t$ with independent components based on the low-frequency observations of the corresponding time-changed Lévy process $L_{\mathcal{T}(t)}$, where $\mathcal{T}$ is a nonnegative, nondecreasing real-valued process independent of $L_t$, is studied. We show that this problem is closely related to the problem of composite function estimation that has recently gotten much attention in statistical literature. Under suitable identifiability conditions, we propose a consistent estimate for the Lévy density of $L_t$ and derive the uniform as well as the pointwise convergence rates of the estimate proposed. Moreover, we prove that the rates obtained are optimal in a minimax sense over suitable classes of time-changed Lévy models. Finally, we present a simulation study showing the performance of our estimation algorithm in the case of time-changed Normal Inverse Gaussian (NIG) Lévy processes.