In this paper we study the exact boundary controllability for the following Boussinesq equation with variable physical parameters: \begin{array}{lll} ρ(x)y_{tt}=-(σ(x)y_{xx})_{xx}+(q(x)y_x)_x-(y^2)_{xx},&&t>0,~x\in(0,l),\\ y(t,0)=σ(l)y_{xx}(t,0)=y(t,l)=0,~~σ(l)y_{xx}(t,l)=u(t)&&t>0, \end{array} where $l>0$, the coefficients $ρ(x)>0,σ(x)>0 $, $q(x)\geq0$ in $[0,l]$ and $u$ is the control acting at the end $x=l$. We prove that the linearized problem is exactly controllable in any time $T>0$. Our approach is essentially based on a detailed spectral analysis together with the moment method. Furthermore, we establish the local exact controllability for the nonlinear problem by fixed point argument.