You can stop counting if you wish, but you cannot stop millis()! :-)
I don´t understand exactly what do you pretend... but if you want to check at what second something happens, make a single call to millis() divided by 1000 when the event is triggered, instead of "duplicating" the information of millis() (although scaled) in secCounter. If you want to have the counter running in the console till something happens set a boolean that tells the program whether to count whether not.

  i.e.:  boolean counting=true
    
          void setup(){ /*whatever here*/}         

          void draw(){
            if (counting){
             secCounter += (millis()/1000);  //notice I´ve changed = onto +=
          void mousePressed(){      //press any mouseButton to toggle counting
             counting=!counting;
          }

What is the best way for counting seconds? I don’t think millis() is a good way.

Because when I use this, once I run the program, millis() start counting. But I want start counting for example when  click mouse. And when for example, press key save the second

Try this one. If you press any mouse button it starts counting, if you press it again counter stops and the result is printed in seconds at the console. You can do it as many times as you want:

boolean counting=false;
int countingBeginning, countingEnd;
float record;

void setup(){}       
 void draw (){}
void mousePressed(){    
  if (!counting) { countingBeginning=millis();}
             else { countingEnd=millis();
                      record=(countingEnd-countingBeginning)*.001;
                      println(record);
                    }
  counting=!counting;
}


Ale · 60rpm.tv/i

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