To protect the reconfigurable scanning network from the influence of unauthorized access, tampering of transmitted data by malicious instruments and sniffing, a lock isolation security structure is proposed. Firstly, the presented structure divides the instruments without security threat to each other into one group, and the groups can be accessed one by one via the isolated signals, which can prevent malicious instruments tampering and sniffing transmitted data. Secondly, the key instruments are protected by the lock segment insertion bit. The lock segment insertion bit can only be opened when multiple key values at specific positions are set to specific values (0, 1 sequence), which can increase the difficulty of unauthorized access. Besides, to reduce the hardware overhead, and the difficulty of place and route caused by excessive instrument groups, instrument grouping algorithm is proposed. The proposed algorithm firstly constructs an undirected graph based on the security relationship among instruments. Then the maximal independent sets of the undirected are obtained. In this way, the number of instrument groups is reduced greatly. Compared to other similar methodologies, the experimental results conducted on ITC 02 benchmark circuits show that the time consumption for opening the locking segment insertion bit of the proposed security structure increased by 7 times, and the average percentage reduction of area, power consumption and wire length is 3.81%, 9.02% and 4.55%, respectively.