The structural changes in the surface layer of p‐type Cz‐Si(001) samples after high‐dose low‐energy (2 keV) He+ plasma‐immersion ion implantation and subsequent thermal annealing were studied using a set of complementary methods: high‐resolution X‐ray reflectometry, high‐resolution X‐ray diffraction, transmission electron microscopy and atomic force microscopy. The formation of a three‐layer structure was observed (an amorphous a‐SiOx layer at the surface, an amorphous a‐Si layer and a heavily damaged tensile‐strained crystalline c‐Si layer), which remained after annealing. Helium‐filled bubbles were observed in the as‐implanted sample. The influence of annealing on the evolution of the three‐layer structure and the bubbles is considered. The bubbles are shown to grow after annealing. Their characteristic size is determined to be in the range of 5–20 nm. Large helium‐filled bubbles are located in the amorphous a‐Si layer. Small bubbles form inside the damaged crystalline Si layer. These bubbles are a major source of tensile strain in the c‐Si layer.