We present S3ML, a secure serving system for machine learning inference in this paper. S3ML runs machine learning models in Intel SGX enclaves to protect users' privacy. S3ML designs a secure key management service to construct flexible privacy-preserving server clusters and proposes novel SGX-aware load balancing and scaling methods to satisfy users' Service-Level Objectives. We have implemented S3ML based on Kubernetes as a low-overhead, high-available, and scalable system. We demonstrate the system performance and effectiveness of S3ML through extensive experiments on a series of widely-used models.