In this paper, we propose a superimposed training based two-phase robust channel estimation scheme for the unmanned aerial vehicle (UAV) assisted cellular communication system, in which various unitarily-invariant channel statistics errors are considered. Specifically, in the first phase, mobile station (MS) estimates the UAV-MS channel via the UAV training sequence, of which the robust design can be solved based on convex-concave theory. While in the second phase, the superimposed training scheme is considered at the ground base station (GBS) to improve spectrum efficiency. Then the robust GBS training sequence, the information signal power and the UAV amplifying factor are jointly optimized for the partially cascaded GBS-UAV-MS channel estimation subject to GBS and UAV transmit power constraints as well as the required information signal strength at the MS. To tackle this NP-hard problem, the optimal structures of involved variables are firstly derived, based on which the robust superimposed training design is simplified and proved to be quasi-convex in the UAV amplifying factor. Particularly, for Spectral norm and Nuclear norm bounded errors, the optimal training sequence can be obtained via convex-concave theory and Golden section searchWhile for Frobenius norm bounded error, a tractable upper-bounding scheme is proposed for the robust superimposed training design. Furthermore, we extend our work into the more general probabilistic path loss scenario of UAV-ground channels, and analyze the impacts of the probabilistic path loss and Rician K-factor on channel estimation performance. Numerical results illustrate the excellent performance of the proposed superimposed training based two-phase channel estimation scheme.