An anomalous nuclear modification was reported by JLab measurements on the beryllium‐9 structure function F2. It is unexpected in the sense that a nuclear modification slope is too large to be expected from its average nuclear density. We investigated whether it is explained by a nuclear clustering configuration in 9Be with two α nuclei and surrounding neutron clouds. Such clustering aspects are studied by using antisymmetrized molecular dynamics (AMD) and also by a simple shell model for comparison. We consider that nuclear structure functions F2A consist of a mean conventional part and a remaining one depending on the maximum local density. The first mean part does not show a significant cluster effect on F2. However, we propose that the remaining one could explain the anomalous JLab slope, and it is associated with high densities created by the cluster formation in 9Be. The JLab measurement is possibly the first signature of clustering effects in high‐energy nuclear reactions. A responsible physics could be an internal nucleon modification, which is caused by the high densities due to the cluster configuration.

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