In this paper, we consider the following two-component Schrödiner system
\[ \begin{cases} -\Delta u_1 +V_1(x) u_1= \mu_1 u_1^{3} +\beta u_1u_2^{2} & \text{in}\;\mathbb{R}^{3},\\ -\Delta u_2+V_2(x) u_2= \mu_2 u_2^{3} +\beta u_1^{2}u_2 & \text{in}\;\mathbb{R}^{3}. \end{cases} \]
First, we revisit the proof of the existence of an unbounded sequence of non-radial positive vector solutions of synchronized type obtained in S. Peng and Z. Wang [Segregated and synchronized vector solutions for nonlinear Schrödinger systems, Arch. Rational Mech. Anal. 208 (2013), 305–339] to give a point-wise estimate of the solutions. Taking advantage of these estimates, we then show a non-degeneracy result of the synchronized solutions in some suitable symmetric space by use of the locally Pohozaev identities. The main difficulties of BEC systems come from the interspecies interaction between the components, which never appear in the study of single equations. The idea used to estimate the coupling terms is inspired by the characterization of the Fermat points in the famous Fermat problem, which is the main novelty of this paper.