We study the di-baryon in the holographic QCD. The di-baryon is composed of six quarks and bound by the color interaction. In this paper, we adopt the Sakai-Sugimoto (SS) model as the holographic QCD to study the di-baryon. The SS model is formulated in a \(\mathrm{D4}/\mathrm{D8}/\overline{\mathrm{D8}}\) system of the Type IIA string theory. It is expected that the di-baryon is described by the 2-instanton configuration of the flavor symmetry on D8-branes since the baryon number is identified as the instanton number. We will construct the 't Hooft 2-instanton solution explicitly and use it to discuss the stability of the di-baryon. An effective action of this model has not only the Yang-Mills (YM) action but also the Chern-Simons (CS) action coming from the CS action of probe D8-branes, and the CS action assigns \(U(1)\) charges associated with the baryon number to each instanton. As a result, we can see that the di-baryon is unstable due to this \(U(1)\) charge in the SS model.