He received $338m (£225m) in time-based awards and $197m (£131m) in performance-related stock when he took over from Steve Jobs in 2011.
Apple's share price hit an all-time high in November last year, valuing his incentive package at $535m (£356.9m).
For the 54-year-old to receive the sum, he must stay in the role until 2021 and keep Apple's shares at or above their current levels. Other performance criteria must also be met.
In its 2014 pay report, Apple said: "The company has traditionally believed that long-term equity awards in the form of (restricted stock units) are the most effective way to attract and retain a talented executive team and to align executives' interests with those of shareholders."
The report also shows that Mr Cook received a 43% pay rise in his basic salary from $1.4m (£930,000) to $2m (£1.3m) in February last year.
His total compensation package doubled last year to $9.2m (£6.1m) - his first pay increase since November 2011.
The package included almost $700,000 (£467,000) paid towards his security expenses, and $56,923 (£37,950) for unused holiday allowance.
The company's entire executive team was given a 14% pay rise last year after impressive results.
Their annual pay rose from $875,000 (£583,500) to $1m (£670,000), and their potential bonus doubled to $4m (£2.7m).
Angela Ahrendts, poached from Burberry last May, was the highest-paid executive at the firm last year, earning $73m (£48.7m).
The sum included $37m (£24.6m) compensation for unvested Burberry equity awards and $33m (£22m) of restricted stock units.
Apple said the stock was used to "encourage Ms Ahrendts to join the company and to provide her with a meaningful equity stake".