The sugar content in watermelon significantly influences its flavor. To understand the sugar accumulation pattern in small-fruited watermelon and identify candidate genes involved in sugar synthesis and conversion, we measured the sugar content (sucrose, fructose, and glucose) at five developmental stages: 10d, 16d, 22d, 28d, and 34d post-pollination. Two watermelon varieties with the largest sugar content difference at 28d post-pollination (high-sugar G38-28 and low-sugar 482276-28) were selected for transcriptome sequencing. Differentially expressed genes (DEGs) were validated using RT-qPCR. Additionally, the sugar contents of three commercial varieties (‘Su Meng NO.5’, ‘Su Meng NO.6’, ‘Su Meng NO.7’) and their parents were compared at five stages. Results showed glucose and fructose levels peaked between 22d and 28d, followed by a decrease, while sucrose content continuously increased. F1 hybrids exhibited glucose and sucrose trends similar to their paternal parent and fructose trends similar to their maternal parent. Transcriptome sequencing identified 9337 DEGs (5072 upregulated and 4265 downregulated). Gene Ontology analysis highlighted overrepresentation in categories such as pectinase and oxidoreductase activity. KEGG analysis identified 12 DEGs involved in sugar synthesis and conversion pathways, including phenylpropanoid biosynthesis and pentose and glucuronate interconversions. RT-qPCR validation corroborated the transcriptome data. These findings explain the distinct sugar accumulation patterns in G38-28 and 482276-28 at the transcriptional level, offering insights for genetic breeding and regulation of key sugar-related genes in watermelon.