Three-dimensional (3D) data are easily collected in an unconscious way and are sensitive to lead biological characteristics exposure. Privacy and ownership have become important disputed issues for the 3D data application field. In this paper, we design a privacy-preserving computation system (SPPCS) for sensitive data protection, based on distributed storage, trusted execution environment (TEE) and blockchain technology. The SPPCS separates a storage and analysis calculation from consensus to build a hierarchical computation architecture. Based on a similarity computation of graph structures, the SPPCS finds data requirement matching lists to avoid invalid transactions. With TEE technology, the SPPCS implements a dual hybrid isolation model to restrict access to raw data and obscure the connections among transaction parties. To validate confidential performance, we implement a prototype of SPPCS with Ethereum and Intel Software Guard Extensions (SGX). The evaluation results derived from test datasets show that (1) the enhanced security and increased time consumption (490 ms in this paper) of multiple SGX nodes need to be balanced; (2) for a single SGX node to enhance data security and preserve privacy, an increased time consumption of about 260 ms is acceptable; (3) the transaction relationship cannot be inferred from records on-chain. The proposed SPPCS implements data privacy and security protection with high performance.