The question can best be answered when you give us some more details about the two ontologies: are they light-weight or heavy-weight, of the same structure, covering which domain of knowledge?
Although, the question is not detailed enough to be answered, a number of methods and tools are available for this purpose. You should read the following book (especially its Part-II), in order to be able to select the best in your case:
Ontology Alignment: Bridging the Semantic Gap (Semantic Web and Beyond)
efficient alignment cannot be done via protégé, it is better to use a dedicated tool to carry out ontology matching.
I recommend you coma 3.0, it is flexible, you can vary alignment parameters to obtain different results, such as the threshold of similarity (between 0 and 1) and it has been around since several years (actively maintained):
coma 3.0 website: http://dbs.uni-leipzig.de/de/Research/coma.html
Ontology Matching is a complex task that involves several basic techniques and strategies that inherit several related specialties derived from Knowledge Engineering in general. Indeed, an alignment method exploits the different components of an ontology (terminological, structural and semantic aspects). Protégé can not provide an effective alignment according to the predescribed principle. There are several alignment tools geared towards this task (see the link below).
In addition, I recommend this reference book in the context of Ontology Matching :
Ijaz Uddin google ensan abhi nahi bana hay es leyay insano say puchna pera. Google baba say nahi bun paya hay, es leyay sawal researchgate per payhnk deya hay, number banany kay leyay nahi. Raha protege tu wo meray kam may kam tek tarha nahi ker raha ta.