In light transmission microscopy, axial scanning does not directly provide tomographic reconstruction of specimen. Phase deconvolution microscopy can convert a raw intensity image stack into a refractive index tomogram, the intrinsic sample contrast which can be exploited for quantitative morphological analysis. However, this technique is limited by reconstruction artifacts due to unoptimized optical conditions, which leads to a sparse and non-uniform optical transfer function. Here, we propose an optimization method based on simulated annealing to systematically obtain optimal illumination schemes that enable artifact-free deconvolution. The proposed method showed precise tomographic reconstruction of unlabeled biological samples.