Joel Manby announced that 2017 will be the last year of the show in San Diego.
He said that the move was part of a strategy that seeks to reverse falling visitor numbers at the company’s 11 parks across the US.
SeaWorld has faced intense criticism by activists who say keeping the orcas in captivity is cruel and unnecessary.
Its shares have halved in value since the release of a critical documentary film two years ago.
Dramatic displays by orcas are the centerpiece at three parks operated by SeaWorld, in California, Florida and Texas.
The San Diego park is the company’s second biggest and features its famous Shamu killer whale show.
The parks have long been criticized by animal rights activists and some politicians, who argue that keeping the mammals – also known as orcas – in captivity is cruel and unnecessary.
Last month, Californian authorities prohibited SeaWorld from breeding animals in captivity, calling into question the future of the park’s popular killer whale attraction.
The San Diego show will reportedly be replaced with a new orca experience in a “more natural” setting but it is not clear what exactly that will involve.
SeaWorld’s popularity was damaged and attendance fell at its parks – especially in California – following the critically-acclaimed 2013 documentary Blackfish, which highlighted the impact of captivity on orcas.
The company has dismissed the documentary as inaccurate and misleading, pointing out that it has not captured a whale in the wild for 35 years.
SeaWorld has since sought to improve its fortunes with a fresh marketing campaign and discount offers.
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