The temple is dedicated to Lord Dhanwanthari, who is regarded by Hindus as the Master-God of Ayurveda - the health science of the east. Temples with Dhanwanthari Idol installation are rare enough, but temples with Lord Dhanwanthari as the presiding deity, are rarer still. Maruthorvattom Sree Dhanwanthari Temple is the first and of foremost importance among such temples of south Kerala.

Lord Dhanwanthari is regarded as a part-incarnation of Lord Vishnu. Lord Vishnu, one among the trinity is regarded as the one managing the maintenance of the universe. Hindu Puranas mention that Lord Dhanwanthari made his appearance from Palazhi (the sea of milk) carrying the bowl of Amruth (the elixir of life and rejuvenation) while Gods and Demons were churning the Palazhi, in search of a remedy for the senility befell on gods as a result of a curse by the rishi Durvasav.

In meditation, Sree Dhanwanthari is visualized as a four-handed, dark-complexioned God carrying Sankha (the holy bugle of Lord Vishnu), Chakra (the revolving blade), the bowl of Amruth (the potion of eternal life and rejuvenation), and Jalooka – the leach used by Ayurvedic practitioners to suck away the vitiated blood from the body.