Apple's compensation committee awarded him a total "target compensation" of $49m (£45.1m) for 2023.
Last year the iPhone maker's shares fell sharply in the face of supply chain issues and a global economic slowdown.
"The Compensation Committee balanced shareholder feedback, Apple's exceptional performance, and a recommendation from Mr Cook to adjust his compensation in light of the feedback received," Apple said in a filing with a US financial watchdog.
The move will see Mr Cook's annual basic salary unchanged at $3m, as well as a bonus of up to $6m.
The biggest difference to his pay package is how he will be awarded shares in the firm.
In 2022 the company granted him $75m of shares, half of which were based on how well Apple performed on the stock market.
For this year his stock award target has been cut to $40m, with three quarters of that dependant on share performance.
The target for Mr Cook's compensation for 2022 was $84m, although his actual total pay for last year was $99.4m. That figure included $630,600 in personal security costs and $712,500 for his use of a private jet.
Last year Apple shareholders were urged by a leading investor advisory group to vote against Mr Cook's pay package.
In a letter to investors, Institutional Shareholder Services (ISS) said there are "significant concerns" over the "design and magnitude" of the package.
The ISS said Mr Cook's pay was 1,447 times more than the wage of an average Apple employee.
Mr Cook became Apple's chief executive in August 2011, just weeks before the death of co-founder Steve Jobs.
Under Mr Cook's leadership Apple became the first company to reach a stock market valuation of $3tn before falling to about $2.1tn during a tumultuous year for the technology industry.
Covid lockdowns at factories in China, supply chain delays and a global economic slowdown have helped push down Apple's share price by more than 20% over the last year.
The 62-year-old's personal wealth stands at around $1.7bn, according to Forbes magazine. Mr Cook has pledged to give away his entire fortune during his lifetime.