(Mini) split supersymmetry explains the observed Higgs mass and evades stringent constraints, while keeping good features of TeV-scale supersymmetry other than the little hierarchy problem. Such scenarios naturally predict thermal wino dark matter whose mass is around $3 , {rm TeV}$. Its non-perturbatively enhanced annihilation is a promising target of indirect detection experiments. It is known that identifying the smallest halos is essential for reducing an uncertainty in interpreting indirect detection experiments. Despite its importance, the smallest halos of thermal wino dark matter have not been well understood and thus are investigated in this work. In particular, we remark on two aspects: 1) the neutral wino is in kinetic equilibrium with primordial plasma predominantly through inelastic processes involving the slightly heavier charged wino; and 2) the resultant density contrast shows larger powers at dark acoustic oscillation peaks than in cold dark matter, which is known as an overshooting phenomenon. By taking them into account, we provide a rigorous estimate of the boost factor. Our result facilitates accurately pinning down thermal wino dark matter through vigorous efforts in indirect detection experiments.