Prad,
Yes, at any given time, the "Junction Temperature" will be the hottest temperature of the silicon chip. However, this temperature can vary anywhere in the "Operating Temperature Range", as specified in the datasheet. For these purposes, we can assume the operating temperature is equivalent to the junction temperature.
It is important to keep the junction/operating temperature within the recommended operating range (-40 to 105°C for an "Extended" device). The Absolute Maximum Operating Temperature (105°C) should never be exceeded to guarantee functionality and lifetime.
For more details, please see http://processors.wiki.ti.com/index.php?title=AM335x_Thermal_Considerations.
Regards, Hieu