The Horton-Strahler (HS) number, a classical measure of branching complexity arising in hydrology and register allocation, is studied for butterfly trees, a recursive family of binary trees generated by block-merging operations. These trees arise as binary search trees of butterfly permutations, which form the $2$-Sylow subgroup of the symmetric group on $N = 2^n$ elements and appear in models of parallel computation and structured Gaussian elimination. For a single merging step applied to two independent Catalan trees with $m$ nodes, we show that HS$(\mathcal T_1 \oplus \mathcal T_2)/\log_2(2m) \to 1/2$ in probability, so the classical Catalan scaling is preserved under this restricted construction. In the simple butterfly model, where each level is formed from identical copies and encoded by an $n$-bit string $\mathbf{x}$, the HS number admits an exact representation as an additive functional of an explicit $8$-state Markov chain driven by iid bits $x_j \sim \mathrm{Bern}(p)$, and can be computed in $\mathcal O(n)$ time from $\mathbf{x}$. This yields a complete limit theory, including a strong law HS$(\mathcal T_n^B)/n \to μ_p = pq/(1-pq)$ almost surely and a functional central limit theorem with variance $σ_p^2 = pq(1 - 3pq - 2p^2q^2)/(1-pq)^3$. For general butterfly trees, obtained by recursively merging independent subtrees, the increment depends on an expanding edge profile, and the process does not admit a finite-state reduction. We give an $\mathcal O(N)$ algorithm to compute the HS number directly from the $(N-1)$-bit encoding, characterize the zero-HS class, and combine exact enumeration for small $n$ with Monte Carlo simulations up to $n=25$, supporting HS$(\mathcal T_n^B)/n \to α\approx 0.4450$ in probability for uniform butterfly trees, placing the general model strictly between the simple butterfly limit $1/3$ and the Catalan limit $1/2$.