Fountain code, as a linear random code without a fixed bit rate, can be introduced into multi-path transmission control protocol (TCP) to improve throughput and reduce the bottleneck effect caused by path quality diversity. However, the multiple-hop transmission of data and huge feedback delay of acknowledge character (ACK) will lead to excessive transmission of fountain-coded packets on multiple paths, posing serious privacy concerns. To tackle with this problem, we propose a secure cross-locking enabled multi-route fountain coding scheme in this paper which can utilize the diversity of transmission quality among different paths to improve the security of the multi-route fountain code transmission system. Specifically, the fountain-coded packet data on the superior path of the legal receiver is employed to protect the fountain-coded packets on the inferior path, forming a cross-interlocking structure between multiple paths. This design can reduce the probability that the eavesdropper receives enough fountain-coded packets and decode successfully. Besides, the data received by the legal receiver is used to support implicit transmission of control information, further reducing the interception probability of eavesdropper. The simulation results finally verify the effectiveness of this scheme against eavesdropping attack.