As a theologian, his fame rests upon his reply to Charles Chauncy upon the salvation of all men, in which he defended the orthodox evangelical doctrine, his reply to Samuel West's Essays on Liberty and Necessity, in which he largely modified his father's theory of the will by giving it a liberal interpretation, and upon his sermons on the atonement. A great deal of religious controversy raged in New England during his lifetime. His works were published at Andover in two volumes, and were later re-published together along with a memoir by Tryon Edwards. Unlike his father, who was a slave-owner, Jonathan Edwards the younger supported abolition of the slave trade and of slavery. His anti-slavery viewpoint was first evidenced in 1773, when he wrote a series of articles entitled “Some Observations upon the Slavery of Negroes” in the Connecticut Journal and the New-Haven Post-Boy. These views were further articulated in his 1791 sermon, "The Injustice and Impolicy of the Slave trade." It was his work and some of Samuel Hopkins's which were among the first direct appeals to the freedom of slaves from the New England ministry. While much of his work was spent defending the works of his father Jonathan Edwards, Joseph Bellamy, and Samuel Hopkins, he was a key part of the 1801 Plan of Union.
Contribution to linguistics
Edwards was a pioneer in the historical linguistics of Native North America. He was raised in the community of Stockbridge, Massachusetts, where Native American speakers of the Mohican language were the majority, and he became fluent in that language as a child. In 1755, Edwards's father sent him to stay in the Iroquois settlement of Onohoquaga, with the purpose of training him for future missionary work. Through this experience, Edwards acquired first-hand knowledge of Iroquoian and other Algonquian languages. In 1787, Edwards published a study of the Mohican language, which he referred to as Muhhekaneew. In it, he chronicled basic vocabulary and grammar rules and recorded the marked differences between Mohican and English. He argued against the misconception that Native Americans had no distinct parts of speech in their language, writing, "It has been said that savages have no parts of speech beside the substantive and the verb. This is not true concerning the Mohegans, nor concerning any other tribe of Indians, of whose language I have any knowledge. The Mohegans have all the eight parts of speech, to be found in other languages; though prepositions are so rarely used, except in composition, that I once determined that part of speech to be wanting." In 1787, Edwards published a study of the Mohican language. In it, he presented evidence for the relatedness of Algonquian languages throughout northeastern North America and their distinctness from the neighboring Iroquoian languages. Edwards' work on New World linguistic classification paralleled that of his contemporary, William Jones, on the Indo-European languages. In his report, "Observation on the Language of the Muhhekaneew Indians...", Jonathan Edwards observes the Mohican language "have no diversity of gender, either in nouns or pronouns". He also observed that Mohican can also use plural forms just by adding an extra morpheme to the singular form. Such as the singular word for boy is penumpaufoo and the plural form is penumpaufoouk for boys. The Mohican language does not contain any adjectives, instead neuter verbs are used to express the qualities.