Many people get confused with these 3 terms- functionalities of MS Project.
Nenad wrote a Blogpost clarifying them and presenting their differences through an example:
Far too often people arbitrarily track project performance through the “Percent (%) Complete” method with subjective estimates for “how finished” the project is. Microsoft Project doesn’t work well with this since manually entering values into the % complete field logically cascades a cavalcade of calculations, which aren’t necessarily intuitive. The % complete or % work complete fields in Project work best when actual hours of labor or actual hours of time passed get entered (but that’s the topic of a different article.) If you wish to use the subjective assessments, the better alternative may be the Physical % Complete field.
The Physical % Complete field is included by default in the Tracking Table (View | Table | Tracking) or it can be inserted into any Task-oriented view (Insert | Column | “Physical % Complete” in the Field name: field). Any values in the Physical % Complete field must be manually entered, and so it’s designed for human operators to insert their own subjective opinion of the relative degree of completion. Unfortunately, this field causes problems when project status needs to be summarized.
Read the post from here: : % Complete VS Physical % Complete in MS PROJECT 2013 | Nenad Trajkovski