As a new generation of economically important fruit, blackberry fruit is rich in nutrients and functional components. However, the ripe fruit is very low in firmness, soft, and perishable. Therefore, storage and preservation have become important factors restricting its industrial development. The overexpression vectors of RuEG1 and RuEG2 encoded endo-1,4-β-glucanase from blackberry were introduced into tomato to identify their functions at different ripening stages. The results showed that firmness of transgenic tomato fruit decreased with the development period. The structure of transgenic tomato collapsed earlier than that of wild-type tomato. The comparison showed that the contents of cellulose, hemicellulose, and pectin in transgenic tomato were significantly reduced compared with wild-type tomato. Pectin methylesterase and cellulase activities were significantly increased in transgenic compared with wild-type tomato. Transcriptome and qRT-PCR data showed that the expression levels of cell wall degrading enzyme genes SlXTH3, SlCel2 and SlCel8 were significantly higher than those of the control. The genes of RuEG1 and RuEG2 regulated enzyme activity in fruit cell walls and influenced cell wall composition, thus regulating fruit firmness and improving fruit quality and storability. In addition, the SlXTH3 and SlCel8 genes were higher expressed in RuEG2 than in RuEG1 transgenic fruits at the yellow fruit stage, which might be the reason why they reveal divergent regulation during fruit ripening stages.