Against the background of the global energy transition and the rapid development of carbon markets, integrated energy systems (IESs) gradually become an important approach to supporting a low-carbon economy through multi-energy coordination and market interactions. However, existing studies do not fully address the asynchronous nature of inter-annual trading and multi-timescale decision-making for IESs in electricity, natural gas, and carbon markets. To address this issue, a multi-timescale optimization decision-making method for IESs considering multi-market asynchrony and uncertainty is proposed. At the annual scale, the proposed method optimizes electricity and natural gas contract trading strategies as well as inter-annual carbon quota banking strategies, and characterizes the inter-annual features of carbon trading according to carbon market compliance rules. At the daily scale, based on the annual-scale optimization results, the operation strategies of park-level energy devices and spot market trading schemes are further refined. By introducing the conditional value-at-risk (CVaR) method, the model quantifies and controls the risks caused by market price fluctuations and uncertainty in carbon emission verification, thereby ensuring the economic efficiency and robustness of the scheduling scheme. Case studies demonstrate the effectiveness of the proposed method in multi-market coordination and multi-timescale decision-making.