The use of physical barriers is a common defensive strategy in small-sized endophagous arthropods, but this feeding mode often results in tracks being left on host organisms, thus increasing predation risk. Mechanisms of escape from tracking predators are thus particularly important for endophagous arthropods. Leaf miners are herbivorous insects that inhabit the interiors of leaves and produce various forms of tracks on their host plants. Such tracks are called “mines,” and parasitoid wasps, which are the primary enemy of leaf miners, use mines as cues to find host larvae. In the present study, we use the leaf-mining moth Acrocercops transecta (Insecta: Lepidoptera: Gracillariidae), which changes mine forms during larval growth, and its primary parasitoid Aneurobracon philippinensis (Hymenoptera: Braconidae). Larvae of A. transecta make narrow linear mines in the first and second instars, the third instars expand the mines to flat blotch mines, and the fourth and fifth instars construct three-dimensional tentiform blotch mines. A laboratory parasitization experiment showed that successful oviposition rates were significantly lower on tentiform blotch mines than on other mine types. In contrast, all fifth instars that were transplanted into flat blotch mines were oviposited, suggesting that older instars did not deter ovipositing parasitoids and that the lower rates of successful oviposition on tentiform blotch mines were attributable to refuges inside such mines provided by their three-dimensional structure. Field data demonstrated a plateau in parasitism rates in fourth instar larvae, confirming the results of the laboratory experiment. These results indicate that different mine forms affect the viability of endophagous larvae.