The Spanish utility said the deal would allow the exchange of information between the two bodies.
Iberdrola will also invest $5 billion in Mexico over the next four years to increase its presence in the market.
It currently has 5.2GW capacity of power generation installed in the Central American country comprising of gas and wind plants.
The deal was signed by Iberdrola chairman Ignacio Galán and Enrique Ochoa Reza, managing director of the commission.
The agreement will allow them to work together on renewable energy projects as well as on conventional power generation sites.
Iberdrola owns the 70MW Dos Arbolitos project in south-east Mexico, which is due to come online later this year, and is involved in six other projects.