Colloidal crystal engineering with DNA has made significant progress in the bottom-up fabrication of long-range ordered three-dimensional superlattice materials with unique optical, catalytic, and biological properties using DNA-functionalized nanoparticles, known as programmable atom equivalents (PAEs), as fundamental building blocks. However, escaping metastable states during the self-assembly of PAEs in far-from-equilibrium systems remains an intractable challenge in this field. As an entropy-modulating strategy, thermal annealing is a widely adopted conventional approach for regulating PAE crystallization. Recently, several alternative or complementary PAE assembly strategies have emerged, particularly catalytic-assembly approaches based on toehold-mediated DNA strand displacement, which enable programmable and efficient synthesis of PAE superlattice structures under mild isothermal conditions. This concept paper reviews and discusses key developments in programmable isothermal regulation strategies, focusing on their operating mechanisms, advances in dynamic functionalities, and representative applications, with the goal of inspiring future research in related fields.