Based on the plant-level dataset of Taiwan 2005-2009 Report on Factory Operation Census, which was collected by Ministry of Economic Affairs, R.O.C. This paper investigated the firm productivity was influenced by different dimensions and levels of agglomeration (labor input, R&D input and proximity).By taking industry structure and proximity into account, we calculated EG Index and NNI to analyze the agglomeration phenomena of Taiwan electronics industry. Results showed: (1) The indices of labor input and R&D input agglomeration both increased. (2) There was a significant positive relationship between R&D input agglomeration and productivity, while the effect of labor input agglomeration on productivity was negative. (3) In general, we found the firms located in the cluster have suffered from the agglomeration diseconomies. (4) The relationships between agglomeration and productivity were affected by the plant-specific features and region-specific characteristics.