Long non-coding RNAs (lncRNAs) are a class of non-coding RNAs that play essential regulatory roles in various developmental processes and stress responses. However, the functions of lncRNAs during the flowering period of tomato are largely unknown. To explore the lncRNA profiles and functions during flowering in tomato, we performed strand-specific paired-end RNA sequencing of tomato leaves, flowers and roots, with three biological replicates. We identified 10919 lncRNAs including 248 novel lncRNAs, of which 65 novel lncRNAs were significantly differentially expressed (DE) in the flowers, leaves, and roots. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were carried out to identify the cis target gene of DE lncRNAs. The results showed that the lncRNAs might play an important role in the growth, development, and apoptosis of flowering tomato plant by regulating the formation of intima in flower tissues, binding to various molecules, influencing metabolic pathways, and inducing apoptosis. Moreover, we identified the interaction between 32, 78, and 397 kinds of miRNAs, lncRNAs, and mRNAs. The results suggest that the lncRNAs can regulate the expression of mRNA during flowering period in tomato by forming competitive endogenous RNA, and further regulate various biological metabolism pathways in tomato.