This paper presents a novel approach to writer adaptation based on convolutional neural network (CNN) as a feature extractor and improved discriminative linear regression for online handwritten Chinese character recognition. First, the proposed recognizer consisting of CNN-based feature extractor and prototype-based classifier can achieve comparable performance with the state-of-the-art CNN-based classifier while it could be designed more compact and efficient as a practical solution. Second, the writer adaption is performed via a linear transformation of the extracted feature from CNN. The transformation parameters are optimized with a so-called sample separation margin based minimum classification error criterion, which can be further improved by using more synthesized adaptation data and a simple regularization method. The experiments on the data collected from user inputs of Smartphones with a vocabulary of 20,936 characters demonstrate that our writer adaptation approach can yield significant improvements of recognition accuracy over a high-performance baseline system and also outperform a state-of-the-art approach based on style transfer mapping especially with increased adaptation data.