for(i=0;;i++)
    {
        struct st_message st[N];
        system("cls");
        getchar();
        printf("请输入所添加学生学号: ");
        gets(st[i].num);
        printf("请输入所添加姓名: ");
        gets(st[i].name);
        printf("请输入所添加班级: ");
        gets(st[i].classs);
        printf("请输入所添加寝室号: ");
        gets(st[i].dorm);
        fwrite(&st[i],sizeof(struct st_message),1,fp);
        printf("输入成功! \n是否继续录入(Y/N)?");
        choice=getchar();
        if(choice=='y'||choice=='Y')
            continue;
        else
        {
            fclose(fp);
            break;
        }
    }

可能是缓冲区没有彻底清除~

这样试试：
    struct st_message st[N];
    int ch;
    for(i=0;i<N;i++)
    {
        system("cls");
        printf("请输入所添加学生学号: ");
        gets(st[i].num);
        printf("请输入所添加姓名: ");
        gets(st[i].name);
        printf("请输入所添加班级: ");
        gets(st[i].classs);
        printf("请输入所添加寝室号: ");
        gets(st[i].dorm);
        fwrite(&st[i],sizeof(struct st_message),1,fp);
        printf("输入成功! \n是否继续录入(Y/N)?");
        choice=getchar();
        while((ch=getchar())!='\n' && ch!=EOF);
        if(choice=='y'||choice=='Y')
            continue;
        else
        {
            fclose(fp);
            break;
        }
    }