1. According to Thomson, the positive charge is uniformly distributed throughout the atom. Whereas according to Rutherford, the positively charged protons are inside the nucleus.
2. According to Thomson, electrons are embedded in the positively charged atom, but according to Rutherford, electrons are revolving around the nucleus in well defined orbits.
3. According to Thomson, electrons are stable inside the atom but according to Rutherford, electrons are moving inside the atom.