An approach to estimate the performance of FPGA architectures is proposed based on semi-supervised model tree algorithm. The proposed approach avoids synthesizing, mapping, packing, placing and routing, which are essential steps in a traditional flow to obtain the performance of FPGA. Thus it is time efficient while the performance predicted maintains quite close to the result obtained through the traditional method (a tool flow called VTR). This can be utilized effectively during the early FPGA design stage to choose an optimal architecture under a certain metric. Comparisons are made between the performance obtained by the proposed approach and by VTR on a commercial 40nm technology. Results show that the proposed approach has MRE below 7.62% compared to VTR, and improves the time cost by thousands of times when utilized in architecture design space exploration.