''Colloidal molecules'' (CMs) represent artificial colloidal clusters replicating the geometries of molecules and exhibiting flexibility and fluctuations similar to macromolecules and proteins. Their dynamic and anisotropy characters make them unique and indispensable building blocks for creating hierarchically organized superstructures in material sciences. Despite the progress in synthesizing and assembling CMs, unveiling their dynamic characters is challenging in experiments. Here, we employ real-time three-dimensional imaging and simulations to reveal dynamic CM structures in micrometre-sized colloidal-emulsion models with tunable electrostatic interactions. Our findings reveal that CMs' dynamic structures are inherently asymmetric, with angular symmetry emerging through continuous ordering from a liquid-like configuration. We further develop a novel method to guide the ordering of CMs towards a desired structure by dynamically adjusting the ionic strength in the solvent during the ordering process. Our research contributes to a clearer physical understanding of dynamic CMs and offers potential solutions to the complexities inherent in their formation process.