Transport for London (TfL) said Mr Wright would be replaced by Mark Wild, currently managing director of London Underground, on 19 November.
Mr Wright is stepping down “as planned” after just eight months in the job, according to TfL.
However, at the time of his appointment in March, he was expected to stay in the job “as it completes its remaining work”.
Crossrail will slash east-west journey times through the capital and is the biggest construction project in Europe.
TfL believes the £15bn project will boost Britain’s economy by an estimated £42bn while adding 10% to central London’s rail capacity.
Originally due to open in December, TfL has blamed the delay to the central section of the line on the need for testing communication between trains and signalling systems.
The central section now will not run until autumn 2019.
Mike Brown, London’s transport commissioner, said: “The Elizabeth line is the single most significant addition to London’s transport infrastructure in a generation.
“It is absolutely vital that Crossrail Ltd completes the job of delivering it safely and reliably for London.
“Mark’s extensive knowledge and experience of delivering major signalling and systems integration projects will be vital for the final stages of the project.”
Last week, transport minister Jo Johnson agreed to loan London Mayor Sadiq Khan £350m to cover additional costs caused by the delays.
Mr Johnson had already announced this year that Crossrail’s budget was being increased from £14.8bn to £15.4bn due to “cost pressures”.
Once completed, Crossrail – to be known as the Elizabeth Line – will take passengers from Abbey Wood, in London’s southeast, to Heathrow Airport in the west of the capital.
Services will also run from Shenfield in Essex to Reading in Berkshire.
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