Should we use custom master pages, custom page layout, custom theme in SP Online? I heard it is not recommended in SP online, is this true? If it is true then what is the main cause for

Hi,

You will your answer hopefully at the link http://blog.sharepointexperience.com/2015/01/to-brand-or-not-to-brand/. Regarding 'what should you do' in the link, you better follow the updated links:

• Customize your SharePoint site UI by using JavaScript
• Follow Patterns and Practice project at Github

The Pattern and Practice project in GitHub will provide you more insight and examples of how you should apply branding.

Pnp says you should not use custom master page in sp online.

I think no one should use it in SP online. Am I correct?

Yes, no one shouldn't as per Microsoft's best practices

so we should not use any of custom master page, custom theme and custom page layouts in SP online?

What is alternative best practice? Please su

• so we should not use any of custom master page, custom theme and custom page layouts in SP online?
  Yes you can use custom theme or page layouts but should not modify master page
• What is alternative best practice? Please suggest.
  I've provided recommended approach in my first post (Use JS/CSS external to master page, and follow GitHub Project for examples/suggestions)

Long story short, instead of modifying master page, load your css/js through custom actions. Please take a look at GitHub project.