How can I implement lookup filters for custom objects in lightning experience?

Hii Rachit,

As of now there is no such LookUp filters available in Lightening Salesforce. There is an idea available for the same issue.

And also this is an well known issue to Salesforce, as this is being mentioned in the Salesforce’16 winter release guide for limitation. You can see it here.

In case you can choose a other work around to get the similar functionality but that might be too tricky and too lengthy. You can create junction object which will act as an filter and holds the value for you.

Thanks.