However, I have just renewed my passport in February this year. After updating my new passport number and submitting my tax returns through the e-filing system, I have trouble logging into my account. A pop-up message has appeared on the page saying "Digital Certification not exist" when I tried to log into my account with my new passport number. 

There are two methods for you to apply your digital certificate: e-CP55D and e-KYC. I would recommend choosing e-CP55D instead of e-KYC. 

Choosing the e-KYC method will require you to download the MyTax app from the app store on my mobile. After you have downloaded the app, you are required to upload your identification document and selfie in the app to verify your identify. Sounds easy, right? However, the app is extremely buggy. I have trouble uploading and verifying my identify in the app. Therefore, I really recommend you to submit the e-CP55D instead. 

After clicking the e-CP55D option, the website will direct you to the First Time Application page. Check your details and proceed to the next page after you have confirmed everything is correct. For people who are logging into the system for the first time, you are required to fill in your details and upload your identification document. Make sure your email address is correct. 

After you click "submit", you should receive an email from LHDN almost instantly. Click the link in the email and it should bring you the page below.

The PIN Number is automatically generated. This is so much easier and faster than before. I wish LHDN has this system in place when I first submitted my tax returns 8 years ago! 

In this page, you just need to type in your new passport number or MyKad number and click "Submit".

Check your basic information and make sure everything is correct. You will need to type in your password and security phase before submitting.