There are two ways to make someone obey you: fear and love. I do not recommend fear, because it will make your married life hell, and you will probably divorce. Therefore, the best option is to encourage her to love you a lot. People will go to no end to obey their beloveds!

However, do keep in mind that obedience can quickly become boring. 

Generally the Qur'anic mention of "disobedience" is taken to mean "infidelity" or "refusing to engage in physical intimacy", and things that stem from that, not obedience in all matters. Beyond that, people have different cultural and personal models of the power dynamics of marriage. Some people enter a marriage with a strong model that a wife should obey a husband in everything, and other people enter a marriage with the idea that marriage is more of a partnership where the two people work together in harmony and consultation for the greater good of the family.

If you have specific issues that you disagree about, and you are unable to come to an agreement or see the other person's side, you could get a third party (a formal marriage counsellor or someone else) to arbitrate. It is natural for people to have differences of opinion on how to live life due to factors such as personality, upbringing, psychological needs, social pressures (which women and men often experience differently), responsibilities, social class, and the like, even if they come from the same religious background. Most people tend to copy whatever model of marriage and family life they saw growing up is and subconsciously assume it is shared by everyone else, whereas every family is different. 

There is also the issue of communication. People are not born with the skill to communicate and it is something that ideally develops over time. When they enter a marriage, some people are very good at identifying and communicating their expectations or wants to their spouse, and others are not, and just react emotionally when their expectations and wants are not met. (This works both ways, I am not directing it at yourself) Indeed many people are not self-reflective enough to really understand why they (or others) do what they do or discuss it analytically, so sometimes having some scaffolding helps. 

If it is a serious issue such as infidelity, a formal marriage counsellor or religious counsellor is also a good idea.