#include<stdio.h>
#include<math.h>
int main(void)
{
    signed number1,number2,number3,a,b,c,max;
    printf("Input 3 number:");
    scanf("%d,%d,%d",&number1,&number2,&number3);
    a=abs(number1);
    b=abs(number2);
    c=abs(number3);
    if(a>b)
    {
        max=a;
        if(a>c)
        {
            max=a;        
        }
        else
        {
            max=c;
        
        }
   
   
    }
    else
    {
        max=b;
        if(b>c)
        {
            max=b;        
        }
        else
        {
            max=c;
        
        }   
    }
    printf("Output:\nThe number with maximum absolute value is %d.\n",max);
    return 0;
}

要告诉别人你输入了什么
假如是“1，-100，90”那肯定不对，应该是“1,-100,90”

运行了没错，就是100啊，你这程序不就是求绝对值最大的数吗？你这的max求的是将三个数转化为绝对值后中最大的数
如果你的意思是要输出绝对值最大的数：改成如下程序
#include<stdio.h>
#include<math.h>
int main(void)
{
    signed number1,number2,number3,a,b,c,max;
    printf("Input 3 number:");
    scanf("%d,%d,%d",&number1,&number2,&number3);
    a=abs(number1);
    b=abs(number2);
    c=abs(number3);
    if(a>b)
    {
        max=a;
        if(a>c)
        {
            max=a;        
        }
        else
        {
            max=c;
        
        }
   
   
    }
    else
    {
        max=b;
        if(b>c)
        {
            max=b;        
        }
        else
        {
            max=c;
        
        }   
    }
    if(max==a)//转换为原来的数
{
  max=number1;
}
else if(max==b)
{
max=number2;
}
else
{
max=number3
}
printf("Output:\nThe number with maximum absolute value is %d.\n",max);
 return 0;
}

signed number1,number2,number3,a,b,c,max;
这个应该是int number1，number2，....
signed是修饰符可省，但是int不可省

可省，参见C标准中Type specifiers节
— void
— char
— signed char
— unsigned char
— short, signed short, short int, or signed short int
— unsigned short, or unsigned short int
— int, signed, or signed int
— unsigned, or unsigned int
— long, signed long, long int, or signed long int
— unsigned long, or unsigned long int
— long long, signed long long, long long int, or signed long long int
— unsigned long long, or unsigned long long int
— float
— double
— long double
— _Bool
— float _Complex
— double _Complex
— long double _Complex
— atomic type specifier
— struct or union specifier
— enum specifier
— typedef name