In this paper, we propose a robust Cholesky factorization method for symmetric positive definite (SPD), hierarchically semiseparable (HSS) matrices. Classical Cholesky factorizations and some semiseparable methods need to sequentially compute Schur complements. In contrast, we develop a strategy involving orthogonal transformations and approximations which avoids the explicit computation of the Schur complement in each factorization step. The overall factorization requires fewer floating point operations and has better data locality when compared to the recent HSS method in [J. Xia and M. Gu, SIAM J. Matrix Anal. Appl., 31 (2010), pp. 2899--2920]. Our strategy utilizes a robustness technique so that an approximate generalized Cholesky factorization is guaranteed to exist. We test three different methods for compressing the off-diagonal blocks in each iteration, i.e., rank-revealing QR, SVD, and SVD with random sampling. In our comparisons, we find that, with high probability, using SVD with random samplin...