how can i say in french we changed the way of counting?

A natural way to say it in French is: Nous avons changé la manière de compter. You could also say:

• Nous avons changé la façon de compter.
• Nous avons modifié la manière de compter.

If you want, I can also give you a version that sounds more formal , casual , or more idiomatic in French.