Studies on evolution have made significant progress in multiple disciplines, but evolutionary theories remain incomplete, controversial and inadequate in explaining origin of life and macroevolution. Here we create the concept of carbon-based entities (CBEs) which include methane, amino acids, proteins, bacteria, animals, plants, and other entities containing carbon atoms. From thermodynamics, we deduce the driving force, the progressive mechanisms, and the major steps of CBE evolution, and hence establish a comprehensive evolutionary theory termed the CBE evolutionary theory (CBEET). CBEET highlights that evolution is driven hierarchy-wise by thermodynamics and favors fitness and diversity. It provides novel explanations for origin of life (abiogenesis), macroevolution, natural selection, sympatric speciation, and animal group evolution in a comprehensive and comprehensible way. It elucidates that collaboration, altruism, obeying rules with properly increased freedom are important throughout the CBE evolution. It refutes thoroughly the notion that negative entropy (negentropy) leads to biological order which is distinct from thermodynamic order. It integrates with research advances in multiple disciplines and bridges laws of physics, evolution in biology, and harmonious development of human society.