Physicalism is a world view supported by modern natural science, and a world view that supports modern values, the concept of happiness and development, and belongs to the tradition of naturalism. The core idea of Physicalism is the idea that everything is physical. With the rapid development of computer science and technology, Computationalism, a kind of Physicalism, is exerting a growing influence. The fundamental view of Computationalism is that the essence of human thought is computation, the mind is a computer, and even the entire universe is a giant computer. Roger Penrose, a Nobel laureate in physics, refuted Computationalism, but remained committed to deterministic Physicalism. Computationalism and Penrose’s Physicalism presuppose mathematical Reductionism and Theory of Complete Knowability of the world. Reductionism and Theory of Complete Knowability are the key points of Physicalism. According to Reductionism and Theory of Complete Knowability, it is man’s duty to conquer nature. However, the construction of ecological civilization inevitably requires mankind to lay down the sword of conquering nature and strive for harmonious coexistence between human civilization and nature. In this sense, Physicalism is a deep ideological obstacle to the construction of ecological civilization. According to quantum mechanics and complexity science, mathematical Reductionism and Theory of Complete Knowability are highly questionable. As a methodology, Reductionism is essential, but it is not necessarily the law of the creation or constitution of the world itself. If nature is always emerging with new things, new structures, new orders, then it is not precisely determined by immutable mathematical laws, and human science cannot exhaust the infinite mysteries of nature.