How to find distance center to center from square $1$ to square $3$, if we need overlap area is $15.46 mm^2$. if we know each side of the square is $6.9 mm$.
Firstly I find the distance is $9.3 mm$ but it's wrong. Anyone can help to solve this question ?

$$L=6.9mm$$ $$A_o=15.46mm^2$$ The width of a single overlap region is thus $x=A_o/L$. The distance between the centers is the original distance, $L/2 + L + L/2$ minus twice the width of an overlap region: $L/2 + L + L/2 - 2 x = 9.3188mm$.
So it seems to me like your answer was correct.
Are you sure that $15.46mm^2$ is the area of a single overlap region, as indicated on your figure, and not of the total overlap?