Background Fruit cracking occurs easily under unsuitable environmental conditions and is one of the main types of damage that occurs in fruit production. It is widely accepted that plants have developed defence mechanisms and regulatory networks that respond to abiotic stress, which involves perceiving, integrating and responding to stress signals by modulating the expression of related genes. ... [Show full abstract] Fruit cracking is also a physiological disease caused by abiotic stress. It has been reported that a single or several genes may regulate fruit cracking. However, almost none of these reports have involved cracking regulatory networks. Results Here, 0, 8 and 30 h irrigation treatments resulted in the differential expression of 1028 mRNAs and 87 lncRNAs in ‘LA1698’ (cracking resistant, CR) at 8 h_vs_0 h, 468 mRNAs and 15 lncRNAs in CR_30 h_vs_CR_0 h, 321 mRNAs and 19 lncRNAs in CR_30 h_vs_CR_8 h; 531 mRNAs and 75 lncRNAs in ‘LA2683’ (cracking susceptible, CS) at 8 h_vs_0 h, 420 mRNAs and 24 lncRNAs in CS_30 h_vs_CS_0 h, 270 mRNAs and 20 lncRNAs in CS_30 h_vs_CS_8 h; and 339 mRNAs and 64 lncRNAs in the two contrasting tomato genotypes at 0 h, 338 mRNAs and 94 lncRNAs at 8 h, and 369 mRNAs and 77 lncRNAs at 30 h. The GO pathways of the differentially expressed mRNAs were mainly enriched in the ‘hormone metabolic process’, ‘cell wall organization’, ‘oxidoreductase activity’ and ‘catalytic activity’ categories. In addition, the lncRNAs regulated the expression of their neighbouring genes, and genes related to tomato cracking were selected to construct a lncRNA-mRNA network influencing tomato cracking. Conclusions This study provides insight into the responsive network for water-induced cracking in tomato fruit. Specifically, lncRNAs regulate the hormone-redox-cell wall network, including plant hormone (auxin, ethylene) and ROS (H 2 O 2 ) signal transduction and many cell wall-related mRNAs ( EXP, PG, XTH ), as well as some lncRNAs (XLOC_010878 and XLOC_016662, etc.).