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Fruit locule number is an important agronomic trait that affects fruit appearance, quality, and yield. <i>CLAVATA3</i> (<i>SlCLV3</i>) is a candidate gene of the <i>fasciated</i> (<i>fas</i>) locus that plays a role in controlling the number of flower organs and fruit locules in tomato. The <i>SlCLV3</i> encoding signal peptide mainly acts by inhibiting the expression of <i>WUSCHEL</i> (<i>WUS</i>) but there is little research about how the receptor transmits the CLV3 signal to <i>WUS</i> and inhibits its expression. The CRISPR/Cas9 method was employed to edit the first exon of tomato <i>SlCLV3</i> in this study, leading to the functional deletion of <i>SlCLV3</i>. As a result, flowers with a high number of organs and fruits with a high number of locules were produced. We screened six candidate genes using the transcriptome of <i>clv3</i> mutants, analyzed expression variations in these genes between the cultivated allele and wild-type allele of <i>fas</i>, and showed that only <i>SlLET6</i> and <i>SlGIF1</i> (<i>GRF1-interacting factor 1</i>) were influenced by the <i>fas</i> locus. <i>SlLET6</i> overexpression resulted in an increase in flower carpels and fruit locules. These results suggest that <i>SlLET6</i> may be the downstream gene of <i>SlCLV3</i> regulating the number of carpels and fruit locules in tomato.