The New York Times NYT 1.09% is moving away from standardized “banner” advertisements on its website and plans to replace them with its own proprietary display ad formats.

Online banner advertising has become increasingly commoditized in recent years, with the same standardized, rectangular formats appearing on sites across the web. Marketers lament the lack of creativity in the format and have started to question its effectiveness, which has driven down ad prices. Meanwhile, platforms such as Facebook and Google have built huge ad businesses with their own proprietary or “native” ad formats and offerings.

Spotting this trend, the Times is rolling out its own cross-device ad format called Flex Frame to modernize its display ad business and improve the experience for both users and marketers.

“The way advertisers are using Facebook is very native, for example, but you haven’t really seen many publishers using that model,” said Sebastian Tomich, senior vice president of advertising and innovation at the New York Times. “There’s a good amount of negativity around the display business in the market now, but it’s a staple for us.”

On Wednesday, the Times will begin phasing out the industry-standard 300x250 and 300x600 pixel banner ads that currently appear on the right-hand side of its desktop webpages.

Instead, the Times will introduce horizontal Flex Frame ads, which will appear along the top of webpages, between paragraphs in article pages and in feeds of content elsewhere across the site. These ads will be designed to better match the Times site, and will dynamically adjust in size and layout across different devices and window sizes.

For instance, a Flex Frame ad for GE might include an image, text and link in a larger rectangular format across the top of an article page. The same components can also be seamlessly reorganized by the Times to appear in a mobile ad between paragraphs that allows the reader to scroll through the three main elements of the ad.

An example of a new Flex Frame ad for GE on a New York Times article page Photo: The New York Times

Mr. Tomich said the Times eventually intends to allow advertisers to buy Flex Frame ads “programmatically” using automated ad buying software, but that it also hopes to charge a premium for those ads.

“The big question for us is how do we develop a premium native display business that still has the benefits of automation,” he said.

Google will be the first advertiser to use the new ad product as part of a sitewide advertising takeover promoting its new Pixel phone, Mr. Tomich said. The Times has been testing Flex Frame units on mobile since last year.

Google is also helping to power the new Times ad units, with new functionality it introduced to its DoubleClick ad-serving product earlier this year. That update allows marketers to provide individual ad components such as text, images and video content, and to have their ads automatically created to fit the native units offered by publishers’ sites.

For ads running on the Times, marketers need only provide a logo, call to action, 65 characters and an image that will then be compiled into an ad which aligns with Times standards, the company said.

Alternatively, the Times’ in-house agency T Brand Studio can also create ads on behalf of clients.

As of this week, standardized 300x250 and 300x600 pixel banner ads will only appear “above the fold,” or near the top, of 30% of the Times’ desktop webpages, Mr. Tomich said. By next year it plans to reduce that number further, depending on advertiser uptake.

Convincing advertisers to make that shift isn’t without risks, however, Mr. Tomich said.

“I think more publishers haven’t made this move because it’s incredibly hard to do when your display business and revenue is on autopilot,” he said. “You have to convince advertisers to change with you.”

Write to Jack Marshall at Jack.Marshall@wsj.com