In the Horndeski's most general scalar-tensor theories the equations of scalar density perturbations are derived in the presence of non-relativistic matter minimally coupled to gravity. Under a quasi-static approximation on sub-horizon scales we obtain the effective gravitational coupling G eff associated with the growth rate of matter perturbations as well as the effective gravitational potential Φ eff relevant to the deviation of light rays. We then apply our formulas to a number of modified gravitational models of dark energy-such as those based on f (R) theories, Brans-Dicke theories, kinetic gravity braidings, covariant Galileons, and field derivative couplings with the Einstein tensor. Our results are useful to test the large-distance modification of gravity from the future high-precision observations of large-scale structure, weak lensing, and cosmic microwave background.