Sample Code:

//Create Document Parent Record
Account acc = new Account(Name='Test Account');
Insert acc;

//Create Document
ContentVersion cv = new ContentVersion();
cv.Title = 'Test Document';
cv.PathOnClient = 'TestDocument.pdf';
cv.VersionData = Blob.valueOf('Test Content');
cv.IsMajorVersion = true;
Insert cv;

//Get Content Documents
Id conDocId = [SELECT ContentDocumentId FROM ContentVersion WHERE Id =:cv.Id].ContentDocumentId;

//Create ContentDocumentLink 
ContentDocumentLink cdl = New ContentDocumentLink();
cdl.LinkedEntityId = acc.Id;
cdl.ContentDocumentId = conDocId;
cdl.shareType = 'V';
Insert cdl;