Housekeeping genes are thought to be consistently expressed in different tissues, and therefore they are commonly used as references to normalize qPCR data. But the expression of these genes has proved to be affected by certain experimental conditions. In this study, we evaluated the stability of 9 housekeeping genes of economically important pest, Bactrocera dorsalis, under the stress of β-Cypermethrin insecticide. Variations in gene expression were identified both in the whole bodies of larvae and in their midguts. The expression level of each housekeeping gene was shown to be quite different in different tissues, and suggested that the expression stabilities of these genes were differentially affected by toxicity stress. The stability of EF1α was evaluated both in the whole body and in the midgut by geNorm ana Norm finder and in both analyses it proved to be the best reference gene. The folds of changes of expression of the housekeeping genes normalized by EF1α were in accordance with the evaluation results. Furthermore, the variations in expression of these genes were found to be tissue specific. Based on this work we selected EF1α as a reliable reference for data normalization in qPCR studies, and concluded that it will be helpful in studies of expression of genes related to the insecticide target or its detoxification under toxicity stimulation.