Question

Capacitance will decrease with increase in potential only if the charge is kept constant.
According to the equation, less is the potential difference, more is capacitance. But when there is less potential difference, then lesser work is done to move a charge and less potential energy is stored.so how does that work out to store energy

Answer 1

Capacitance is actually the ratio of charge and potential, as you see in the equation $C=\frac{Q}{V}$
This ratio is a constant, however, so if you take a capacitor and increase the voltage the charge will also increase to compensate, and keep the ratio constant. The capacitance will not change. The same thing happens when you alter any of the quantities, the other one changes to compensate.
$C=\frac{2Q}{2V}=\frac{4Q}{4V}$
The value of the capacitance is actually determined only by the physical characteristics of the capacitor.
The equation for that is:
$C=A\times \frac{ϵ}{d}$
A $\Rightarrow$ Area of the plates
d $\Rightarrow$ Separation between the plates
$ϵ\Rightarrow$ electric permittivity in the space between the plates. (This changes if a dielectric is placed.)
Notice how there is no charge (C) or voltage (V) term in this equation, and hence the capacitance does not depend on the charge or the voltage.