I’m Lizzy, a Guru on Shopify’s support team.
There isn't a way within the admin to bypass the 100 variant per product limit. However there are a few options to get around this, depending on how you'd like to have your products set up.
The first would be to set up different products for segments of the variants. For example if you had a shirt that was blue and red with lots of sizes, you could set up different coloured products with just sizes as variant options. This could work well if you have a small product catalogue.
Another way to have over 100 variants would be to use an app. We have a variety of product option apps available in the app store. Each one uses a slightly different approach to how they set up your variants, so I suggest taking a look to see which would suit your business the best. I've linked a few below for your to check out.
The final way would be quite manual, but could work for some products. With several themes you have the option to enable order notes. You can do this in the theme customizer by going to Online Store>Themes>Customize>Cart Page. On the product page you could request customers specify details about the variant in the cart order notes. This can be a good set up when your products have custom options or require a bit of extra information from the customer.
I hope one of these helps to get your products set up with all the variants you need. Let me know if you have any other questions about this.
Lizzy | Shopify Guru
Lizzy | Social Care @ Shopify
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If it's only for a few products you could look at joining multiple products together (with theme code) to create a giant product. This post is super old but the concept still holds up:
Very likely would need to be tweaked for whatever theme it is you're using.