Mr Cook's salary rose to $2m (?1.3m) from $1.4m, and his total remuneration more than doubled to $9.2m in 2014.
The base salaries for other executives were also increased by over 14% to $1m, the company said in its annual report.
Apple's New York listed shares had hit a record high last year, while almost 40 million iPhones were sold.
The increase to Mr Cook's salary was the first since November 2011. He became the firm's chief executive in August 2011.
In the report, Apple said the increases were given after reviewing "peer company" market data provided by its independent compensation consultant.
The executive team's bonuses were also increased to a maximum of 400% of the member's salary.
In November, Apple was worth more than $700bn after its stock hit an all-time high of $119.75.