There are more similarities than differences between the two cities. However, I list two differences between Harappa and Mohenjodaro below:
1) Geographic Location.
The ancient city of Mohenjodaro (Mound Of The Dead) is situated on mounds located in the modern-day Larkana district of Sindh province in Pakistan. Harappa is located southwest of Sahiwal (150 miles away from Lahore and 250 miles from Karachi). Both are the two greatest cities of the Indus Valley civilization or Harappan civilization.
2) Sculptures and artifacts.
Mohenjodaro is well known for its bronze dancing girl figurines and the statue of the priest-king. Harappa is known for its red and gray sandstone torso figurines. There appear to be no parallels or similarities between the figurines found in both cities. The Great Bath of Mohenjodaro is the largest known public water tank in the ancient world; it may have been used for ritual bathing purposes during its day.
Here are public bathing platforms in Harappa similar in kind to the ones used for washing clothes in some traditional cities in Pakistan and India today.
Both cities were more alike than different in layout and construction. The same type of bricks were used in constructing both Mohenjodaro and Harappa. The earliest artifacts found in both cities were stone seals with elegant animal artwork and Indus script carved into them. A few Indus valley stone seals were also found to have included swastikas, religious symbols prevalent in Hinduism, Buddhism, and Jainism. Phallic symbols and stone seal incarnations of the Hindu god Shiva were also discovered.