Mr Cook was paid $8.75m (Â£7.1m) in salary and bonus in 2016, down from $10.3m the previous year.
All Apple's named executives saw their salary and bonus payments fall after the company reported lower sales and income in the year to September.
However, Mr Cook also received $136m from the sale of shares.
The information is contained in a filing lodged with the US financial regulator, the Securities and Exchange Commission.
Mr Cook has been Apple chief executive since August 2011.
As part of his contract, he was awarded shares in the company which could only be "vested" or sold at stipulated times. It is these which have now brought his overall earnings close to $145m.
Each of the other named executives including chief financial officer Luca Maestri and Angela Ahrendts, senior vice president of retail received nearly $23m in salary, down from about $25m in 2015.
In its SEC filing Apple said it had produced strong financial results in 2016.
"However, the two financial measures used to evaluate executive performance under our annual cash incentive program, net sales and operating income, declined from our record-breaking 2015 levels.
"These results were below the target performance goals set by the Compensation Committee. As a result, the annual cash incentive payouts to our named executive officers were below target," it added.
It said cutting the cash incentive payouts reflected "strong pay-for-performance alignment".
In 2016 Apple reported net sales of $215.6bn, 7.7% lower than in 2015. Operating income came in at $60bn, 15.7% below the previous year.
Mr Cook's base salary was $3m, and the annual base salary for each of the other named executive officers was $1m.
Apple chief executive Tim Cook saw his salary and bonus slide in the last financial year, but his income from the sale of shares jumped dramatically.