Background <p>This study aims to quantitatively analyze retinal crystalline deposits in patients with Bietti Crystalline Dystrophy (BCD) and examine their progression over time in a longitudinal study.</p> Methods <p>We retrospectively reviewed consecutive patients diagnosed with BCD at a single center. Retinal crystalline deposits were quantified from fundus photographs using semi-automated software, which divided the macular area into a central foveal circle, inner ring, and outer ring. We then analyze changes in the area and area fraction of these deposits over a two-year period.</p> Results <p>The study included 30 eyes from 16 patients. Over the two-year study period, the inner ring demonstrated the statistically significant decrease in both crystal area and crystal area fraction from baseline to one year (<i>P</i> = 0.044 for area; <i>P</i> = 0.003 for area fraction) and two years (<i>P</i> = 0.003 for area; <i>P</i> &lt; 0.001 for area fraction). Mean crystal area fraction was 1.042 ± 0.295% in the central foveal circle, 1.056 ± 0.208% in the inner ring, and 1.001 ± 0.155% in the outer ring, with no significant differences observed between the regions (all <i>P</i> &gt; 0.05). The genotype-phenotype correlation showed that exon7del homozygotes had significantly lower baseline crystal area and area fraction, suggesting an association with more severe disease.</p> Conclusions <p>The use of semi-automated software to analyze fundus photographs provided a quantitative method for assessing retinal crystalline deposits in BCD. This longitudinal study enhanced our understanding of the disease’s natural progression.</p>