Obtaining quartz nanocrystals (NCs) of high purity and uniform sizes remains a challenging problem. In this report, the synthesis and characterization of quartz NCs under hydrothermal conditions was investigated and the corresponding mathematical models were introduced to elucidate the growth kinetics of quartz NCs. Amorphous silica nanoparticles were dissolved in aqueous solutions followed by mild hydrothermal reactions, resulting in NCs with relatively uniform sizes and shapes. The NCs were made from highly crystalline α-quartz. Their hydrothermal growth process over an induction period of ~3 hr initially yielded amorphous silica nanoparticles that were aggregated into clusters. The crystallinity of α-quartz emerged from the products of the nanoparticle clusters after the induction period, which likely involved an amorphous to crystalline transition. The NCs continued to grow with increasing time. The growth kinetics exhibited a dependence on the square root of time, which has not been observed for other quartz nanocrystalline systems. The analysis suggests that the process is reaction-limited, not diffusion-limited, likely governed by the dissolved silicate monomer flux to the surface of the growing NCs followed by first-order rate-limiting attachment kinetics. This study highlights the growth kinetics of quartz NCs by unveiling the complex nature of multistep growth processes, offering an improved hydrothermal method for fine-tuning the size and morphology of quartz NCs, which have potential optoelectronics, sensing, and rechargeable battery, and novel biorefinery process applications.