Citrus viroid V, (CVdV), with 293-294 nucleotides length, belongs to the genus Apscaviroid from the family Pospiviroidae. It is one of an infectious viroids in citrus. Small RNAs (sRNAs) with 20-24 nt length, have been play important role in regulation of biosynthesis process and metabolic process in plants. For identification and characterization of the small RNAs whose generated in response to CVdV infection, small RNAs were extracted from healthy and infected tomato (Solanum lycopersicum) and two libraries were constructed using CATS (Capture and Amplification by Tailing and Switching) method and sequenced in Illumina Hi-Seq 2500 platform. The adaptors and low-quality reads were removed from the reads, refined reads were aligned against the viroid genome and tomato reference genome (SL2.0.50). Identification of purpose mRNAs for each microRNA and their functional role were carried out using the plantgrn website (http://plantgrn.noble.org). MicroRNAs were identified using the miRbase database. Analysis of the results revealed a total of 28 conserved microRNAs and 13 novel miRNA were responsive against CVdV infection in tomato. The identified microRNAs were targeted 188 genes in tomato transcriptome; these genes are involved in the regulation of biosynthetic processes, cellular components metabolism and catabolism, regulation of transcription, response to biotic and abiotic stress, hormonal responses, signal transduction and some other cellular activities. Also, the identified small RNAs were interfered in Flavonoids, Phenyl propanoids, and Linolenic acid pathways which can disrupted the plant's defense system. On the other hand, the small RNAs generated in response to CVdV infection by regulating the activity of transcriptional factors, signal proteins (especially serine-threonine protein kinases) and proteins which involve in auxin signaling alters in plant metabolism, growth and development, and provides the appropriate conditions for development of the disease in the plants.