I have a MSc degree, want to apply for PhD degree. Should I submit my BSc transcript during admission?
Go ahead and submit your undergraduate transcript.  The admissions committee will be expecting to see one and your application might be screened out before consideration simply because this transcript is missing.  

The fact that you've had good grades in your master's program may help you to overcome the bad impression left by your poor undergraduate GPA.  Having good letters of recommendation and one or more publications (of high quality) will help a lot more.