I need to modify a picture with pink color.
I need to modify a picture by pink color.
I need to modify a picture using pink color.
Which one is right?
It depends what you mean.
or more naturally,
This sentence could be interpreted as saying you need to modify a picture by adding the color pink, either to change an existing color to pink or to mix it with pink (e.g. a black-and-white version of the Komen Foundation logo). It could also be interpreted as saying you need to modify in some unspecified way a picture which already contains the color pink (e.g. a picture of a carnation).
This sentence explicitly says you will apply the color pink to the picture, but I don't think sounds as natural as using "with."
The last example,
is not typically used in English.
I would use modify a picture with pink or modify a picture using pink but not modify a picture by pink.