Taiwan investment in MainlandChinaover the last 20 years has shown uneven distribution characteristics in the eastern, central and western regions. What factors led to this type of investment pattern? Did this characteristic continue or change after ECFA? Based on statistical data and the investment conditions, this paper used Moran’s I index analysis method to measure the heterogeneity of the spatial distribution ofTaiwaninvestment in MainlandChinaover 20 years. Then the study applied ordinary and spatial panel analyses to discuss impacting factors of nearly three years ofTaiwaninvestment in MainlandChina. The outcome shows thatTaiwaninvestment in MainlandChinahad a double-fixed timing effect and special effect during the last three years, which impactedTaiwaninvestment in different regions. Finally, this study proposed the regional strategy choices of theTaiwaninvested enterprise in MainlandChinain the future at four levels.