void _object_set_associative_reference(id object, void *key, id value, uintptr_t policy) {
    // retain the new value (if any) outside the lock.
    ObjcAssociation old_association(0, nil);
    id new_value = value ? acquireValue(value, policy) : nil;
    {
        AssociationsManager manager;
        AssociationsHashMap &associations(manager.associations());
        disguised_ptr_t disguised_object = DISGUISE(object);
        if (new_value) {
            // break any existing association.
            AssociationsHashMap::iterator i = associations.find(disguised_object);
            if (i != associations.end()) {
                // secondary table exists
                ObjectAssociationMap *refs = i->second;
                ObjectAssociationMap::iterator j = refs->find(key);
                if (j != refs->end()) {
                    old_association = j->second;
                    j->second = ObjcAssociation(policy, new_value);
                } else {
                    (*refs)[key] = ObjcAssociation(policy, new_value);
                }
            } else {
                // create the new association (first time).
                ObjectAssociationMap *refs = new ObjectAssociationMap;
                associations[disguised_object] = refs;
                (*refs)[key] = ObjcAssociation(policy, new_value);
                _class_setInstancesHaveAssociatedObjects(_object_getClass(object));
            }
        } else {
            // setting the association to nil breaks the association.
            AssociationsHashMap::iterator i = associations.find(disguised_object);
            if (i !=  associations.end()) {
                ObjectAssociationMap *refs = i->second;
                ObjectAssociationMap::iterator j = refs->find(key);
                if (j != refs->end()) {
                    old_association = j->second;
                    refs->erase(j);
                }
            }
        }
    }
    // release the old value (outside of the lock).
    if (old_association.hasValue()) ReleaseValue()(old_association);
}

我们可以看到所有的关联对象都由AssociationsManager管理，而AssociationsManager定义如下：

class AssociationsManager {
    static OSSpinLock _lock;
    static AssociationsHashMap *_map;               // associative references:  object pointer -> PtrPtrHashMap.
public:
    AssociationsManager()   { OSSpinLockLock(&_lock); }
    ~AssociationsManager()  { OSSpinLockUnlock(&_lock); }

    AssociationsHashMap &associations() {
        if (_map == NULL)
            _map = new AssociationsHashMap();
        return *_map;
    }
};

AssociationsManager里面是由一个静态AssociationsHashMap来存储所有的关联对象(类)的。这相当于把所有对象（类）的关联对象都存在一个全局map里面。而map的的key是这个对象的指针地址（任意两个不同对象（类）的指针地址一定是不同的），而这个map的value又是另外一个AssociationsHashMap，里面保存了关联对象的实例变量的key-value对。
而在对象的销毁逻辑里面，见objc-runtime-new.mm:

最后：
untime的销毁对象函数objc_destructInstance里面会判断这个对象有没有关联对象，如果有，会调用_object_remove_assocations做关联对象的清理工作。

参考：
深入理解OC后半部分文章