Sulfur element plays a pivotal role in plant growth and development. Recently, we have demonstrated that miR395 is crucial for the sulfate homeostasis through regulating the sulfate uptake, transport and assimilation in Arabidopsis thaliana. miR395 controls the sulfate concentration in the shoot by targeting three ATP sulfurylase genes (APS), which encode the first enzymes catalyzing sulfate activation in sulfur assimilation pathway. Furthermore, miR395 also regulates the transport of sulfate between leaves. Under sulfate starvation conditions, upregulated miR395 represses the expression of SULTR2;1, which then confined the transport of sulfate from mature to young leaves. Of note, transcript expression analysis suggested that, unlike APS1 and APS4 mRNA, APS3 and shoot SULTR2;1 is in accordance with miR395 in response to sulfate deprivation. We proposed that the differential regulation of targets by miR395 may be required for adaptation to the sulfate deficiency environment. In addition, our results revealed that there is reciprocal regulation between SULTR2;1 and APS genes through miR395.