The present teaching relates to searching encrypted data. In one example, a search request is received for encrypted documents. An encrypted query is generated based on the search request. The encrypted query is sent to a server that stores a first encrypted index and a second encrypted index. The first encrypted index maps encrypted keywords to full blocks each of which has a same size and is fully filled with encrypted document identities (IDs). The second encrypted index maps encrypted keywords to partial blocks each of which has the same size and is partially filled with encrypted document IDs. Based on the encrypted query, one or more encrypted document IDs are determined by searching against both the first encrypted index and the second encrypted index. A search result is generated based on the one or more encrypted document IDs. The search result is provided in response to the search request.