Van der Lijn was born in Alkmaar, possibly in 1608. He went, in 1627, as Assistant to Batavia, Dutch East Indies aboard the Wapen van Hoorn. From 1632 to 18 January 1636 he was Accountant-General. In 1639 he became Counsellor-Extraordinary to the. A year later he was appointed President of the Schepenrechtbank. One further year later he was made a full Counsellor he followed Philips Lucasz as Director-General of the Indies.
Shortly before his death on 19 April 1645, Governor-General Antonio van Diemen called upon the Dutch Council of the Indies to establish Cornelis van der Lijn as his successor. This was not in line with the instructions of the , who has laid down in 1617 that immediately after the death of a Governor-General, the Council should choose a provisional Governor-General. Only once the Seventeen Lords had agreed to the choice would the appointment come into actual force. The Heren XVII at first cancelled Van Diemen's decision, but then afterwards named the very same Cornelis van der Lijn as his successor. On 10 October 1646 he was named by them as Governor-General. Cornelis van der Lijn was not a strong ruler. He built a little on what his predecessor Van Diemen had established, but did not go much further. He signed peace treaties with Solor, Bantam and Mataram. Moreover, on 24 September 1646 he signed a agreement with the Prince of Mataram, the first of such contracts signed by the Dutch with Javanese rulers. Strenuous measures were taken to maintain the monopoly of the Dutch East India Company in the Moluccas. After a fierce struggle, the fortress at Kapaha on Thitu Island was taken. The severe regulations would soon lead to riots. The rulers in the Netherlands allowed Van der Lijn, at his own request, to retire with honour on 7 October 1650. Carel Reyniersz was then named as Governor-General. In 1651, Cornelis van der Lijn left aboard the Prinses Royaal for the Netherlands. His reception in the homeland was as cool as his departure from the Indies. The customary reception and congratulations given to a returning fleet and its commander were denied to him.
Mayor of Alkmaar
He established himself in Alkmaar where he was elected Mayor on 24 December 1668. He died there on 27 July 1679.
