Convolutional Neural Networks (CNNs) based algorithms have been successful in solving image recognition problems, showing very large accuracy improvement. In recent years, deconvolution layers are widely used as key components in the state-of-the-art CNNs for end-to-end training and models to support tasks such as image segmentation and super resolution. However, the deconvolution algorithms are computationally intensive which limits their applicability to real time applications. Particularly, there has been little research on the efficient implementations of deconvolution algorithms on FPGA platforms which have been widely used to accelerate CNN algorithms by practitioners and researchers due to their high performance and power efficiency. In this work, we propose and develop deconvolution architecture for efficient FPGA implementation. FPGA-based accelerators are proposed for both deconvolution and CNN algorithms. Besides, memory sharing between the computation modules is proposed for the FPGA-based CNN accelerator as well as for other optimization techniques. A non-linear optimization model based on the performance model is introduced to efficiently explore the design space in order to achieve optimal processing speed of the system and improve power efficiency. Furthermore, a hardware mapping framework is developed to automatically generate the low-latency hardware design for any given CNN model on the target device. Finally, we implement our designs on Xilinx Zynq ZC706 board and the deconvolution accelerator achieves a performance of 90.1 GOPS under 200MHz working frequency and a performance density of 0.10 GOPS/DSP using 32-bit quantization, which significantly outperforms previous designs on FPGAs. A real-time application of scene segmentation on Cityscapes Dataset is used to evaluate our CNN accelerator on Zynq ZC706 board, and the system achieves a performance of 107 GOPS and 0.12 GOPS/DSP using 16-bit quantization, and supports up to 17 frames per second for 512x512 image inputs with a power consumption of only 9.6W.