Taiwan marine cage aquaculture originated in Penghu and has been developed over 25 years. The expansion of marine cage scale has caused ecological impacts such as enrichment and changes in marine cage sustainable development. The object of this study is to investigate the approaches for assessing the condition of marine cage aquaculture sediment and impacts in Chaiyuan, Penghu. Study methods including cumulative depth and deposit rate of sediment, heavy metals (Cr, Cu, Ni, Pb, Zn, As, Al, Fe, Mn), sulfide, Redox, and Total Organic Carbon were carried to investigate the impact of environment in marine cage aquaculture. Furthermore, Principal Component Analysis (PCA) and Cluster Analysis were implemented to determine the trend of impact distance and depth within the cage areas. This result shows that the average cumulative depth of sediment is approximately 49cm. Cumulative depth and deposit rate of sediment are positive related. The deposit rate of sediment is 0.061g/cm2 per day that is faster than cage farming areas in other countries. The monitoring results from Chaiyuan had the higher concentration of heavy metal than non-farming area. This suggests that the sediment in Chaiyuan has seriously impacted by the cage waste deposition. In particular, higher values of Cr and Ni could be resulted from the discharge of other sources that is needed for further study. High concentration of sulfide was observed under farming cage, Redox from all sites are negative, and the amount of total Organic Carbon is many times than non farming areas. Those conclude that the sediment in Chaiyuan has faced significant III degradation and over its carrying capacity. Contamination of Heavy metal is detected on all the monitoring sites over the farming areas. The higher concentration of heavy metal was observed at the deeper water. The distance, depth and distribution of heavy metal have closely inter-relationships. This study also attempts to provide the approaches of mitigation for improving the farming environment, for example, 1) the authorization should assist farmers in dealing with waste disposal. 2) Implementation of rotation cage farming scheme and integrated multi-trophic aquaculture. 3) Assessment of marine cage carrying capacity and impact to the environment. Those questions should be all taken into concern to achieve the economic and environment sustainable development in the future.