The initial allocation of tradable carbon emission allowances is among the most contentious issues in developing an emission trading scheme (ETS). China faces serious dilemmas of system complexity and information incompleteness and asymmetry in allocating carbon allowance among enterprises. As one of the pilot ETS regions, Shenzhen has launched the first regional cap-and-trade ETS (SZ ETS) in China. Adhering to the overall plan and classification analysis, SZ ETS intends to solve the aforementioned dilemmas by developing innovative allowance allocation policies. A fundamental principle is to allocate allowances based on carbon intensity and actual output, according to which a two-step allocation procedure is constructed. A competitive game mechanism is introduced for allowance allocation among manufacturing enterprises. Empirical results indicate the following: (1) Carbon allowance allocation based on carbon intensity and actual output can mitigate carbon emission growth by reducing CO2 emitted per unit output, and, thus, buffer the shocks of unexpected economic fluctuations to ETS stability; (2) Competitive game allocation may contribute to improving the use of scattered information to enhance the efficiency of information and emission resource allocation. Exploring SZ ETS may provide a reference for formulating future national carbon allowance allocation policies in China and other developing regions.