The emergence of order is a ubiquitous phase transition in nature—spanning materials families from the biological to the atomic—yet, our understanding of spontaneous phenomena such as crystallization remains incomplete. The relationship between interactions of constituents and their resultant configuration during crystal growth and assembly is currently non-predictive, and cannot be understood without knowledge of system dynamics—accessed only by experiments or simulations. So far, existing models of crystal growth focus only on simple, common crystals and are unable to describe how complex structures—those with more than one local motif in their unit cell—form from an isotropic fluid. Understanding how local structure evolves during phase transformations of complex structures is critical for finding broadly applicable principles for crystal growth and engineering assembly pathways for target structures of soft mesoscale materials. Throughout this work, a class of isotropic pair potentials with multiple attractive wells is used to simulate the formation of complex structures beyond ordinary close-packed crystals. This dissertation begins with a review of computational methods for understanding self-assembly, with a focus on alchemical manipulations for probing thermodynamic landscapes and machine learning-based order parameters. Drawing from this, the work presented here builds upon both these directions. A spherical harmonics-based descriptor is presented in a novel application to the crystal growth and assembly of various types of complex structures—ranging from low- to high-coordinated motifs—to describe structural stages through growth pathways. The relationship between the coordination numbers of local motifs in the liquid and solid phases are elucidated and further explored using a geometric algebra-based attention mechanism that shows distinct global structural signatures—from local information only—for pre-crystallization liquids that form different crystal structures. Finally, induced perturbations via change of particle interactions are utilized to study how particular isotropic pair potentials respond to out-of-equilibrium configurations by undergoing liquid–solid or solid–solid phase transformations. Altogether, this thesis aims to shed light on how systems governed by simple interactions "choose" structural configurations through both crystallization and solid–solid phase transformations.