方東樹《漢學商兌》為清代漢宋之爭之名著，然稍後著成之《跋南雷文定》更反映了方氏的理學觀、工夫觀、乃至於對宋明以來學術發展的理解與詮釋。簡言之，方氏之「心」、「意」關係回歸朱子，然以「意」為善去惡的念頭，「誠」則是決絕落實之的動力，道德意向濃厚。方氏更強調「慎獨」的「品節、限制」之義，工夫樣態嚴肅而惕厲。書中並確立以《大學》傳承為基礎的由孔子至曾子、程朱的道統，明儒與漢學考據皆為悖逆之異端。方氏更重新定義〈道學傳〉的內涵，使清初以來〈道學傳〉的取消，由原先對程朱的打擊一躍而化為對程朱的表彰，並成為其逐陸王心學、考證漢學於儒門正宗外之判教依據。這些都是《漢學商兌》中未曾見到、或尚未發展成熟的觀點。

Fang Dongshu and his Hanxue Shangdui played an important role in the conflict of Hanxue (漢學) and Songxue (宋學) in the middle Ching. There were plenty of studies focused on his sharp reprimand and debate to the scholars of Hanxue displayed in Hanxue Shangdui. Nonetheless, his another book Ba Nanlei Wending included more abundant resources which could reflect his concept, theory of self-cultivation, and standpoint of Neo-Confucianism. In short, the exegesis of “mind (Xin)” and “will (Yi)” of Fang was strongly inclined to Zhuxi, though the interpretation of “sincerity (Chengyi)” was innovatively changed. Fang’s concept of “vigilance in solitude (Shendu)” was transformed as a supplementary method of “chengyi”, and the meaning of restriction was extraordinarily emphasized. The viewpoint of the development of Neo-Confucianism was also constructed in Ba Nanlei Wending, most prestigious scholars in the Ming dynasty and the middle Ching was regarded as heterodoxy. More over, Fang redefined the definition of “Neo-Confucianism biography (Daoxue Zhuan)” for the abrogation of it in History of Ming (Mingshi).