#include "stdafx.h"
#include "stdio.h"
#include "stdio.h"
struct student
{
    long num;
    float score;
    struct student *next;
};

struct student *del(struct student *head1,struct student *head2)//第一个链表可以删除相同的num;
{
    
    struct student *p1,*p2,*p3;
    for(p2=head2;p2!=NULL;p2=p2->next)
    {
        for(p1=head1;p1!=NULL;p3=p1,p1=p1->next)
        {
            if(p1->num==p2->num)               
            {
                if(p1==head1) head1=p1->next;     
                else p3->next=p1->next;         
            }
        }
    }
    return(head1);
}
struct student *del_1(struct student *head1,struct student *head2)//为什么第二个链表相同的num不能删除？
{
    struct student *p1,*p2,*p3;
    for(p2=head2;p2!=NULL;p2=p2->next)
    {
        for(p1=head1;p1!=NULL;p3=p1,p1=p1->next)
        {
            if(p1->num==p2->num)
            {
                if(p2=head2)
                    head2=p2->next;
                else
                    p2->next=p2;
            }
        }
    }
}
int main(int argc, char* argv[])
{
    struct student a,b,c,d,e,f,*head1,*head2,*p,*q,*w;
    a.num=99101;a.score=89;
    b.num=99102;b.score=90;
    c.num=99103;c.score=91;
    head1=&a;
    a.next=&b;
    b.next=&c;
    c.next=NULL;
    p=head1;
    printf("第一个链表为:\n");
    while(p!=NULL)
    {
        printf("%ld%5.1f\n",p->num,p->score);
        p=p->next;
    }
    d.num=99103;d.score=92;
    e.num=99104;e.score=93;
    f.num=99105;f.score=94;
    head2=&d;
    d.next=&e;
    e.next=&f;
    f.next=NULL;
    q=head2;
    printf("第二个链表为：\n");
    while(q!=NULL)
    {
        printf("%ld%5.1f\n",q->num,q->score);
        q=q->next;
    }
    head1=del(head1,head2);
    printf("删除后的第一个链表为：\n");
    for(p=head1;p!=NULL;p=p->next)
    {
       printf("%ld%5.1f\n",p->num,p->score);
       
    }
    head2=del_1(head1,head2);
    printf("删除后的第二个链表为：\n");
    while(q!=NULL)
    {
        printf("%ld%5.1f\n",q->num,q->score);
        q=q->next;
    }
    
    return 0;
}

……你第一次已经把链表1中相同的学号的节点删除了，第一次删除的时候当然已经没有了
应该修改删除链表的函数，相同的，两个都一起删除。