What is the difference between M.Sc in CS and MCA? Which one is better?

MCA is advanced in M.Sc. in CS. I will advise you to pursue MCA because it has better career options than M.Sc. If you want to be a teacher than M.Sc. is better option because it has detailed theory syllabus that will be helpful for you in teaching line, MCA is more practical and good for profession

Cannot exactly answer the difference between the two but MCA is a better option. MCAs are equivalent to computer engineers and get better job opportunities. MCA can be a super-set.