In this paper, we study the blow-up analysis of an affine Toda system corresponding to minimal surfaces into S4. This system is an integrable system which is a natural generalization of sinh-Gordon equation. By exploring a refined blow-up analysis in the bubble domain, we prove that the blow-up values are multiple of 8π, which generalizes the previous results proved in [39,37,27,22] for the sinh-Gordon equation. More precisely, let (uk1,uk2,uk3) be a sequence of solutions of−Δu1=eu1−eu3,−Δu2=eu2−eu3,−Δu3=−12eu1−12eu2+eu3,u1+u2+2u3=0, in B1(0), which has a uniformly bounded energy in B1(0), a uniformly bounded oscillation on ∂B1(0) and blows up at an isolated blow-up point {0}, then the local masses (σ1,σ2,σ3)≠0 satisfyσ1=m1(m1+3)+m2(m2−1)σ2=m1(m1−1)+m2(m2+3)σ3=m1(m1−1)+m2(m2−1)for some(m1,m2)∈Z eitherm1,m2=0, 1 mod 4, or m1,m2=2, 3 mod 4. Here σi:=12πlimδ→0limk→∞∫Bδ(0)eukidx.