The millionaire businessman, 73, this week spoke of his intention to sell the club rather than hand down to his family when he decides to retire.
Whelan has overseen the rise of Athletic from the fourth tier to the Premier League during his time in charge.
But he has no intention of stepping aside just yet and Martinez is looking forward to continuing their partnership.
Martinez, 37, said: "We always have that short-term plan and long-term ambition. It is important to bring that stability to the football. We always work with those things in mind.
"We have reduced the wage bill this season and we want to be in a very strong position.
"Every year we are in a healthier way - we develop our squad and improve our aims. That is always the case.
"Our chairman is the reason why Wigan Athletic are in the Premier League. He has made all this possible.
"We will always try to work towards the present and the future.
"It is very important that all Wigan fans know we have got a long-term strategy.
"The club is getting stronger and stronger month by month."
Whelan bought then Third Division Wigan in 1995 and Martinez arrived as a player soon after.
One link with that era was lost last week with the death of John Benson, who was on the coaching staff at the time and later became manager.
Martinez said: "I worked with John when I arrived in 1995 when he was assistant manager.
"He then had different roles, going through to manager, director of football, general manager.
"He spent the best part of 12 years with our football club.
"It was a really sad day when we found out. It caught us by surprise and it was a real shock.
"We are going to try to pay the right tribute on Saturday."
Wigan travel the short distance to Ewood Park to face Blackburn in the Premier League this weekend.
Both sides are in need of victory, with Blackburn 18th in the table and Wigan just a place above them.
The fixture will also have extra poignancy for Whelan, who famously broke his leg playing for Blackburn in the 1960 FA Cup final.
Martinez said: "They are the two football clubs our chairman has been involved with.
"These games are always a special time for our chairman and there are many reasons that make the game extra special.
"You look at the situation of the two football clubs, the amount of points we both have.
"It is a game that means a lot at this stage of the season."