Critics often point out that this synthesis of Confucian, Taoist, and Buddhist ideas hardened over time into a rather rigid moral and social framework. The strong emphasis on li (principle), ritual propriety, and hierarchical roles is said to have encouraged conformity, moral dogmatism, and a conservative social agenda that reinforced existing power structures. This included legitimizing strict hierarchies between ruler and subject, father and son, and husband and wife, thereby supporting patriarchal norms and limiting opportunities for women. Such a system could suppress individuality, discourage critical thinking, and impose a heavy psychological burden through constant demands for self-scrutiny and moral rectification.

On the philosophical side, many have argued that Neo-Confucianism drifted away from the more practical and humane concerns of early Confucianism into elaborate metaphysical speculation. The intricate theories of li and qi, while intellectually impressive, were often seen as overly abstract, making the tradition difficult for ordinary people to access and turning spiritual cultivation into something bookish and scholastic. Internal tensions, such as how a pure and perfect principle could coexist with moral evil manifesting through material force, led to competing interpretations among different schools and raised questions about the coherence of the system. In this sense, the very synthesis of Confucian ethics with Buddhist and Taoist metaphysics sometimes appeared philosophically unstable.

There is also a long-standing critique that Neo-Confucianism, while drawing heavily from Buddhist and Taoist insights, did not fully honor the spirit of those traditions. Its reworking of Buddhist and Taoist concepts into a moralizing Confucian framework has been described as a partial or distorted integration, one that misunderstood key ideas such as Buddhist non-duality or Taoist spontaneity. From this perspective, what might have been a rich dialogue among traditions became instead a selective appropriation, subordinating other paths to Confucian ethical aims. This contributed to the use of Neo-Confucian orthodoxy as a tool for marginalizing alternative spiritual practices and reducing intellectual pluralism.

Finally, the social and institutional impact of Neo-Confucianism has drawn significant criticism. Its dominance in the civil service examinations fostered an educational culture centered on rote memorization and standardized interpretations of canonical texts, which many see as stifling creativity, innovation, and independent inquiry. The combination of intellectual elitism, political orthodoxy, and rigid moral expectations could create an atmosphere where dissenting voices and new ideas struggled to take root. For those seeking a more open, exploratory spiritual life, this legacy is often viewed as both a profound achievement in moral philosophy and a cautionary tale about the costs of turning a spiritual synthesis into an inflexible orthodoxy.