Pyrethroid resistance has become one of the largest obstacles to mosquito control, and Anopheles sinensis is the main malaria vector in China and southeast countries. miRNAs play important roles in many biological processes in insects; however, the diversity and regulation of miRNAs associated with pyrethroid resistance are still little understood at the whole-genome level. This study performed the sequencing and analysis of miRNAs relative to pyrethroid resistance in An. sinensis for the first time, and identified 328 miRNAs, of which 247 are new. A total of 39 miRNAs are identified to be significantly downregulated commonly in all three pyrethroid-resistant populations investigated in comparison to the susceptible strain. There are 7475 genes to be predicted to be targeted by the 39 significantly down-regulated miRNAs, and they were enriched to seven pathways. The regulation of Transferrin by asi-miR-87 was verified using dual-luciferase, and the asi-miR-87 might be involved in P450 pyrethroid detoxification with the affection of iron ion transportation and synthesis through Transferrin. In addition, nine miRNAs were identified to be positively relative to eight genes. This is the first systematic study on the diversity and regulation of miRNAs associated with insecticide resistance at the whole-genome level, and provides an information frame for the understanding of miRNAs and their function in insecticide resistance.