Reducing thermal conductivity ($kappa$) is an efficient way to boost the thermoelectric performance to achieve direct solid-state conversion to electrical power from thermal energy, which has lots of valuable applications in reusing waste resources. In this study, we propose an effective approach for realizing low $kappa$ by introducing lone-pair electrons or making the lone-pair electrons stereochemically active through bond nanodesigning. As a case study, by cutting at the (111) cross section of the three-dimensional cubic boron arsenide (c-BAs), the $kappa$ is lowered by more than one order of magnitude in the resultant two-dimensional system of graphene-like BAs (g-BAs) due to the stereochemically activated lone-pair electrons. Similar concept can be also extended to other systems with lone-pair electrons beyond BAs, such as group III-V compounds, where a strong correlation between $kappa$ modulation and electronegativity difference for binary compounds is found. Thus, the lone-pair electrons combined with a small electronegativity difference could be the indicator of lowering $kappa$ through bond nanodesigning to change the coordination environment. The proposed approach for realizing low $kappa$ and the underlying mechanism uncovered in this study would largely benefit the design of thermoelectric devices with improved performance, especially in future researches involving novel materials for energy applications.