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Weak S···O bonding, a specific noncovalent interaction, plays crucial roles in fields as diverse as molecular recognition, crystal engineering, and biological systems. This article presents an ab initio investigation of a series of dimeric complexes formed between formaldehyde and several sulfur-containing molecules as electron accepters. The bond-length change, interaction energy, topological property of the electron density, and charge transfer of these S···O bonds have been systematically investigated. Moreover, a comprehensive search for nonbonded S···O interactions in proteins was also performed. It was found that the O atom shows a strong intrinsic tendency to approach S from the backside of the R–S bond (in the σs* direction); the S atom tends to approach the O atom either from the orientation of the lone pair of O (in the no direction) or from the vertical direction (in the πo direction). Besides, the linearity of this interaction was further substantiated by the statistical study. As suggested by the results presented in this study, S···O contacts may control protein structures to some extent and the unique directional properties of S···O interactions could be applied in supermolecular assembly and biological design.