High energy light-ion (3.8MeV He) bombardment is used to introduce lattice defects in a 3-dimensional (3D) interconnected network of graphene aerogels (GAs). When these materials are used as anodes for lithium ion batteries, we observe improved percentage reversible capacity and cycle stability compared to those without ion-beam treatment. Furthermore, all ion-beam treated 3D graphene samples exhibit substantially higher Coulombic efficiencies, suggesting at beneficial role of vacancy-type defects in stabilizing solid-electrolyte interphases. Although 3D graphene exhibits initial reversible capacities that are 2–3 times higher than that of graphite (∼372mAh/g), fast capacity fading is observed but becomes more stable after ion-beam treatment. Our experimental results demonstrate that ion-beam treatment is an effective route to tune and produce good-performance graphene electrodes, and that vacancy-type defects help to promote reversible lithium storage capacity in graphene. We further observe that 3D GAs irradiated to the highest dose studied (1016cm−2) fail rapidly upon electrochemical cycling, likely caused by the excessive ion-beam damage and graphene restacking. Raman I(D)/I(D′) signature is considered linked to defect type in graphene and thus is proposed, for the first time, as an indicator of the reversible capacity for GAs.