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Safeguarding privacy in machine learning is highly desirable, especially in collaborative studies across many organizations. Privacy-preserving distributed machine learning (based on cryptography) is popular to solve the problem. However, existing cryptographic protocols still incur excess computational overhead. Here, we make a novel observation that this is partially due to naive adoption of mainstream numerical optimization (e.g., Newton method) and failing to tailor for secure computing. This work presents a contrasting perspective: customizing numerical optimization specifically for secure settings. We propose a seemingly less-favorable optimization method that can in fact significantly accelerate privacy-preserving logistic regression. Leveraging this new method, we propose two new secure protocols for conducting logistic regression in a privacy-preserving and distributed manner. Extensive theoretical and empirical evaluations prove the competitive performance of our two secure proposals while without compromising accuracy or privacy: with speedup up to 2.3x and 8.1x, respectively, over state-of-the-art; and even faster as data scales up. Such drastic speedup is on top of and in addition to performance improvements from existing (and future) state-of-the-art cryptography. Our work provides a new way towards efficient and practical privacy-preserving logistic regression for large-scale studies which are common for modern science.