You should look at a simple problem in classical mechanics.
A Hamiltonian is (rather sloppy) called "time-independent" if it is not "explicitly time-dependent", i.e. if ∂H/∂t = 0; that means that the time-dependence is hidden in the canonical variables. For the simple harmonic oscillator H ~ p² + x² the canonical variables p,x carry (implicitly) time-dependence via the e.o.m., but ∂H/∂t = 0 and b/c of conservation of energy dH/dt = 0.
The Klein-Gordon-Hamiltonian is "time-independent" in the same sense, i.e. ∂H/∂t = 0.
Remark: what you have written down is not really the Hamiltonian, which generates the e.o.m., but only the energy. In a Hamiltonian you have to eliminate the velocities and express everything in terms of generalized positions and momenta, i.e. in terms of φ(x,t) and π(x,t) ~ ∂0φ(x,t). Therefore H = H[φ,π] and the e.o.m. for φ and π are derived via the commutators [H,φ] and [H,π], respectively.
For a time-independent system the canonical e.o.m. of an operator A are generated solely via commutators [H,A]. Therefore the time-dependence of H i.e. dH/dt is generated via [H,H] which is zero, of course.